University of Helsinki on Michael’s Domain

Courses I teach

Fri, 26 Jan 2024 00:00:00 +0000

IN RED - as (one of the) responsible teacher(s); * - as course developer

Current wet lab teaching
*DPDR-305 (1 ECTS) Purification of Recombinant Proteins and Protein Drugs by FPLC Introduction Methods Protein tags PROV-004 (5 ECTS) Introduction to cell and molecular biology methods Alternative assignment: Expression, purification and functional testing of Phusion polymerase Practical: PCR Work PROV-410* (4 ECTS)** Recombinant DNA technology in therapeutic protein engineering - laboratory work

Current wet lab teaching

DPDR-305* (1 ECTS) Purification of Recombinant Proteins and Protein Drugs by FPLC
PROV-004 (5 ECTS) Introduction to cell and molecular biology methods
- Alternative assignment: Expression, purification and functional testing of Phusion polymerase
- Practical: PCR Work
PROV-410* (4 ECTS) Recombinant DNA technology in therapeutic protein engineering - laboratory work

Current courses
FARM-310 (5 ECTS) Biopharmaceuticals, basic course Luento #3: Terapeuttiset proteiinit I: Insuliinit ja insuliinianalogit Lecture #3: Therapeutic proteins I: Insulin ja insulin analogs Luento #4: Terapeuttiset proteiinit II: Erytropoietiini, interferonit, & G-CSF Lecture #4: Therapeutic proteins II: Erythropoietin, interferons, & G-CSF Luennot #5+#6: Terapeuttiset proteiinit III: Vasta-aineet ja fuusioproteiinit Lectures #5+#6: Therapeutic proteins III: Antibodies and fusion proteins PROV-004 (5 ECTS) Introduction to cell and molecular biology methods Lecture #1: Alternative Assignment: Protein Production & Purification Lecture #2: Protein Purification Methods Lecture #3: Protein Purification Tags Lecture #4: PCR lecture *PROV-409 (1 ECTS) Recombinant DNA technology in therapeutic protein engineering - lecture & exercise course Session #1: Introduction to Recombinant DNA Technology: Restriction Enzymes, PCR, Plasmids, Transformation Session #2: Multifragment assembly (“Gibson” and similar), Golden Gate, mutagenesis methods, CRISPR/Cas systems Session #3: Databases, sequences, software, bioinformatics for your cloning Session #4: Vectors and systems for protein expression Session #5: How to make transgenic organisms and recombinant viruses PROV-216 (5 ECTS) Molecular Pharmacology VEGFs and VEGF receptors PROV-204 (5 ECTS) Biological Drugs II Antibodies, antibody fusions and antibody conjugates as drugs TMED-929* (1-2 ECTS) Drug discovery & development with a focus on biologics Introductory lecture Protein drugs group work kick-off Vaccines, vaccine development & biological warfare: The smallpox vaccine Challenges in formulation, production and quality control Evidence-based medicine, science-based medicine, and complementary and alternative medicine PROV-303 (5 ECTS) Advanced Biopharmaceutics Session #6: Biological barriers: The blood brain barrier Session #8: Recombinant DNA Technology (aka “cloning”) is the starting point for nearly every biological drug …and much more Session #9: Transgenic animals: For drug production, generating human antibodies and making animal models of human diseases Session #10: Protein Drugs: Engineering and Case Studies GMB-401 (5-10 ECTS) Integrative health biosciences Clinical Trials MPHARM-002A/PROV-105A (11 ECTS) Drug development and preclinical evaluation Discovery, Development and Optimization of Protein Drugs MPHARM-002B/PROV-105B (11 ECTS) Pharmaceutical product development and rational use of medicines Biophamaceuticals - Challenges in formulation, production and quality control MPHARM-009 (5 ECTS) Introduction to research methods in drug discovery and development – theory Plans for the future… Protein production and purification Stable cell line generation FARM-314 (5 ECTS)** Medicinal preparations I Basic Issues in the Formulation of Biophamaceuticals

Current courses

FARM-310 (5 ECTS) Biopharmaceuticals, basic course
- Luento #3: Terapeuttiset proteiinit I: Insuliinit ja insuliinianalogit Lecture #3: Therapeutic proteins I: Insulin ja insulin analogs
- Luento #4: Terapeuttiset proteiinit II: Erytropoietiini, interferonit, & G-CSF Lecture #4: Therapeutic proteins II: Erythropoietin, interferons, & G-CSF
- Luennot #5+#6: Terapeuttiset proteiinit III: Vasta-aineet ja fuusioproteiinit Lectures #5+#6: Therapeutic proteins III: Antibodies and fusion proteins
PROV-004 (5 ECTS) Introduction to cell and molecular biology methods
- Lecture #1: Alternative Assignment: Protein Production & Purification
- Lecture #2: Protein Purification Methods
- Lecture #3: Protein Purification Tags
- Lecture #4: PCR lecture
PROV-409* (1 ECTS) Recombinant DNA technology in therapeutic protein engineering - lecture & exercise course
- Session #1: Introduction to Recombinant DNA Technology: Restriction Enzymes, PCR, Plasmids, Transformation
- Session #2: Multifragment assembly (“Gibson” and similar), Golden Gate, mutagenesis methods, CRISPR/Cas systems
- Session #3: Databases, sequences, software, bioinformatics for your cloning
- Session #4: Vectors and systems for protein expression
- Session #5: How to make transgenic organisms and recombinant viruses
PROV-216 (5 ECTS) Molecular Pharmacology
- VEGFs and VEGF receptors
PROV-204 (5 ECTS) Biological Drugs II
- Antibodies, antibody fusions and antibody conjugates as drugs
TMED-929* (1-2 ECTS) Drug discovery & development with a focus on biologics
PROV-303 (5 ECTS) Advanced Biopharmaceutics
GMB-401 (5-10 ECTS) Integrative health biosciences
- Clinical Trials
MPHARM-002A/PROV-105A (11 ECTS) Drug development and preclinical evaluation
- Discovery, Development and Optimization of Protein Drugs
MPHARM-002B/PROV-105B (11 ECTS) Pharmaceutical product development and rational use of medicines
- Biophamaceuticals - Challenges in formulation, production and quality control
MPHARM-009 (5 ECTS) Introduction to research methods in drug discovery and development – theory
FARM-314 (5 ECTS) Medicinal preparations I
- Basic Issues in the Formulation of Biophamaceuticals

Teaching Videos
2025 Biologiset Lääkkeet (in Finnish) (Unitube) Biologiset lääkkeet: Intro ja historia Linkki Biologiset lääkkeet: Tuotanto, stabiilius, säilytys ja käsittely Linkki Biologiset lääkkeet - Biosimilaarit, biobetterit ja lainsäädäntö Linkki Esimerkkejä biologisista lääkkeistä Biologiset lääkkeet - Metaboliset sairaudet Linkki Biologiset lääkkeet - Syövän hoitoon tarkoitetut vasta-aineet Linkki Biologiset lääkkeet - Vasta-ainekonjugaatit Linkki Biologiset lääkkeet - Bispesifiset vasta-aineet Linkki Biologiset lääkkeet - Vasta-aineet Alzheimerin taudin hoitoon Linkki Biologiset lääkkeet - Tulevaisuus Linkki

Teaching Videos

2025 Biologiset Lääkkeet (in Finnish) (Unitube)
1. Biologiset lääkkeet: Intro ja historia Linkki
2. Biologiset lääkkeet: Tuotanto, stabiilius, säilytys ja käsittely Linkki
3. Biologiset lääkkeet - Biosimilaarit, biobetterit ja lainsäädäntö Linkki
Esimerkkejä biologisista lääkkeistä
1. Biologiset lääkkeet - Metaboliset sairaudet Linkki
2. Biologiset lääkkeet - Syövän hoitoon tarkoitetut vasta-aineet Linkki
3. Biologiset lääkkeet - Vasta-ainekonjugaatit Linkki
4. Biologiset lääkkeet - Bispesifiset vasta-aineet Linkki
5. Biologiset lääkkeet - Vasta-aineet Alzheimerin taudin hoitoon Linkki
1. Biologiset lääkkeet - Tulevaisuus Linkki

Previous wetlab teaching
2014 - 2019 DPBM-135 Purification and Characterization of Recombinant Proteins (organized yearly until Covid-19) 2015 2017 2015 - 2017 DPBM Cloning Club (wetlab part) 2014 DPBM Practical Molecular Biology and Genetic Engineering (wetlab part) 2010 HBGS Tags in protein expression, detection and purification

Previous courses
2018-2022 DPBM-119 Protein Interaction Biochemistry 2018 Cell-based assays for protein interaction detection & quantification 2022 Cell-based assays for protein interaction detection & quantification 2017 DBPM CancerBio Summer School A short histrory of antiangiogenic tumor treatment 2014 DPBM Practical Molecular Biology and Genetic Engineering (lecture part) 2011 Lymphatic Research lecture series (six lectures) Lecture #1: Introduction to Lymphatic Research

Previous courses

2018-2022 DPBM-119 Protein Interaction Biochemistry
- 2018 Cell-based assays for protein interaction detection & quantification
- 2022 Cell-based assays for protein interaction detection & quantification
2017 DBPM CancerBio Summer School
- A short histrory of antiangiogenic tumor treatment
2014 DPBM Practical Molecular Biology and Genetic Engineering (lecture part)
2011 Lymphatic Research lecture series (six lectures)
- Lecture #1: Introduction to Lymphatic Research

Workshops
2015 - 2017 DPBM Cloning Club (workshop part)

Inauguration of the new professors

Thu, 28 May 2026 00:00:00 +0000

We - the new professors in the Faculty of Pharmacy at the University of Helsinki - gave our inaugural lectures yesterday!

I am focusing on the wrong things

Wed, 22 Apr 2026 00:00:00 +0000

This is a rant, but hear me out. Instead of working on how to utilize AI in my own field, I am:

The Study Voucher

Sat, 04 Apr 2026 00:00:00 +0000

Since I am working at the University of Helsinki (UH), I should probably know a bit more about the upcoming Study Voucher pilot (Finnish: opintoseteli), as UH will offer a lot of courses within this program, including some of mine, e.g. the Recombinant DNA Technology (aka “Cloning”) course. I did some reading, and here is the gist of it:

My Samsung Work Phone Came Preinstalled With Spyware

Thu, 25 Dec 2025 00:00:00 +0000

Working at the University of Helsinki, you might get the impression that the IT department is serious about protecting your digital safety. For example, the IT department forces all UH employees to take a yearly “exam” to prove that we still remember the basics of computer security and privacy. They also continue – against all experts’ advice – to force users to update their passwords annually. Studies have shown that both above practices are lowering and not increasing the security posture [1,2]. Privacy is more of a theater than reality in today’s digital world [3]. Should I have been surprised that the Android phone model officially recommended by my own IT department came preinstalled with spyware?

Still wondering what to study?

Sat, 20 Dec 2025 00:00:00 +0000

This is what I would do if I were 20 years old today: I would enter an interdisciplinary study program. My favorite among the programs offered in Finland is the International Master’s Programme in Pharmacy (officially “Master’s Programme in Pharmaceutical Research, Development and Safety”, abbreviated MPHARM) at the University of Helsinki. I give you 5 compelling reasons:

The Finnish Dream: A Pipe Dream?

Mon, 15 Dec 2025 00:00:00 +0000

A reality check for international students

Finland has been celebrated as the world’s happiest country for now eight years in a row . However, Finland is not only the happiest country, but also the country with one of the lowest fertility rates . In order to stabilize the pension system , Finland decided that it needs immigration, an idea very radical for a country that was 30 years ago almost as isolated from the rest of Europe as North Korea is nowadays from the rest of Asia. At that time, the international car sign for Finland was still SF for Soviet Finland (just kidding, the S obviously stands for Sweden). Finland wants to increase immigration by attracting foreign students to pursue degrees in Finland, hoping that some of them will stay in the country after graduation. Hence, Finland has become an increasingly popular destination for international students, particularly from Asia. Lured by promises of a high-quality life, excellent education, and abundant opportunities, many invest big time to pursue a degree in one of the Finnish universities . Ten years ago, university education was free for everybody (including all foreigners), but since since 2017, students from non-EU/EEA countries have needed to pay tuition fees . This was not the universities’ own decision, but mandated by the government.

Quiz results

Thu, 06 Nov 2025 00:00:00 +0000

Thank you, Aalto-Helsinki iGEM team!

Sun, 02 Nov 2025 00:00:00 +0000

I am extremely proud of you, Aalto-Helsinki iGEM team ( https://www.aaltohelsinki.com )! Although being in survival mode all year long, the results are truly exceptional: Gold Medal achieved, nominated for Best Therapeutics Project (overgrad series, tightly beaten by the equally exceptional Toronto University’s Mystiphage project), and two special prizes for Best Measurement and Best Sustainable Development Impact! I would have loved to be in Paris for the Grand Jamboree, but teaching duties and grant application deadlines took priority. Judging from the videos, I was not required at all. An oral vitamin B12 supplement that also works for all patients currently requiring injections is one step closer. We will keep you informed about our progress, this is only the beginning!

Academic career

Sun, 03 Aug 2025 00:00:00 +0000

A tiny job market but the best European country to live in (considering global warming)

This month, I transitioned from Associate to Full Professor at my university. Trusting the opinion of my doctoral supervisor Kari Alitalo , my current supervisor , and mostly everybody else, I did not prepare a plan B, in case I would be denied tenure. As a Gen Xer on the Finnish job market, what could have been a realistic plan B? Looking at the international job market would make it easier to solve the problem by increasing opportunities by a factor of 100, even when considering only English- and German-speaking countries. Finland’s population is only about 5.6 million, and its job market is tiny. However, going abroad is not that easy if the rest of your family is opposed to a change of scenery. And why would I leave the only country in Europe whose summer temperatures are not health-threatening? Sure, global warming also hits the Nordic countries: We just had the longest uninterrupted heatwave in Finland since people are taking measurements (22 days of >30°C). But 30°C beats 40°C hands down. For my American friends & family: 30°C = 86°F, 40°C = 104°C.

Learning and Teaching Materials about Biological Drugs

Sun, 08 Jun 2025 00:00:00 +0000

Lecture slides “Biologiset lääkkeet” (Finnish)

Learning Materials in Finnish Language

Basic introduction to biological drugs

Title: Biologiset lääkkeet (Biological Drugs) Year: 2016 Creator: Fimea (Finnish Medicines Agency) URL: https://fimea.fi/laaketurvallisuus_ja_tieto/biologiset-laakkeet
Title: Biologiset lääkkeet (Biological Drugs) Year: 2023 Creator: Terveyskylä (Public information service provided a.o. by Finnish university hospitals) URL: https://www.terveyskyla.fi/laaketalo/tietoa-laakkeista/biologiset-laakkeet

Basic introduction to biosimilars

A better Levodopa

Sat, 31 May 2025 00:00:00 +0000

Saku Renunanen’s manuscript about novel inhibitors of levodopa decarboxylases was published in the European Journal of Pharmaceutical Sciences . It is a textbook example of drawing from the expertise of many different people to make progress. We all know that levodopa provides only symptomatic treatment and that the real breakthrough in Parkinson’s Disease treatment probably has to come from a molecular understanding of the formation of the alpha synuclein and tau protein aggregates and how to interfere with or reverse it. However, disentangling the molecular aetiology of Parkinson’s disease and finding a way to interfere with it will still take us many years. Therefore, improving existing treatment strategies can have a bigger impact on patients’ lives in the short term, and exploring new approaches to improve dopamine deficiency-addressing strategies is thus worthwhile.Levodopa is still the go-to drug for Parkinson’s disease, but a lot of it gets broken down before it ever reaches the brain. While we already use drugs like carbidopa (Lodosyn) to help prevent this, recent research suggests that gut bacteria may also be contributing to the issue. Specifically, Enterococcus faecalis and similar bacteria can interfere with their tyrosine decarboxylase enzymes.To address this, in this paper, over 150,000 compounds were screened computationally looking for ones that could block this bacterial enzyme. After a series of in silico and lab tests, three promising compounds were selected that can inhibit both the bacterial TyrDC and human AADC (the enzyme is already targeted in patients).Why does this matter? These compounds could lead to more effective symptomatic treatments for Parkinson’s Disease. Due to differences in the gut microbiome, some patients might benefit more than others, notably those with high levels of levodopa-hungry gut bacteria. Check out the full study here: https://doi.org/10.1016/j.ejps.2025.107133 . I always learn a lot of new, super-interesting things in these types of collaborations. Which is one of the reasons why I chose to do science for a living in the first place.

ProxyJump

Thu, 01 May 2025 00:00:00 +0000

Since OpenSSH 7.3, it has been much easier to connect from the outside to Linux computers inside the UH network. With older ssh versions, you needed to use a complicated “ProxyCommand”, but now it is straightforward:

Billion-dollar gamble

Fri, 28 Feb 2025 00:00:00 +0000

Last December, Forbes published a feature article about Megan Baldwin’s work to improve the antiangiogenic treatment of eye diseases. I hope she wins her billion-dollar gamble not only because the drug in question was invented here at the University of Helsinki. The drug is called OPT-302 or with its INN name sozinibercept. The patent lists Kari Alitalo and me as the inventors. The drug was initially designed (under the name VGX-300) for cancer treatment, but - perhaps luckily - never really took off as such because it inhibits not only VEGF-D but also VEGF-C, which is needed in the body’s immune response against the cancer. So far, nobody has been able to separate the prometastatic and the proimmunogenic propeties of VEGF-C.

The DTE protein asporin and gut regeneration

Thu, 13 Feb 2025 00:00:00 +0000

Aging and regeneration are two of the most fascinating areas of life science. The somewhat obscure protein (or rather proteoglycan) Asporin, previously known, e.g., to regulate TGF-beta activity in cartilage, has now been shown to play a key role in the regeneration of the intestine. An impressive demonstration of scientific grit, Sharif & Pekka! This paper has been in the making for many years, and there were multiple technical challenges to overcome. Sawan K. Jha started this collaboration in 2017 by creating several cell lines before he succeeded with the recombinant production of Asporin. There is no generally accepted definition for the term “difficult to express (DTE) protein”, but Asporin fits the description well. It has miserable yields, and its activity is easily lost during purification. Sawan also produced and purified the first batches, and after Sawan had moved on to Red-Horse Lab at Stanford University , Sharif (upstream) and I (downstream) shared the production and purification work. Here is the direct link to the publication, which should work until April 26, even if you do not have a subscription. After that, use https://doi.org/10.1016/j.stem.2025.02.009 . If you don’t have a subscription, I will happily send you the PDF by email…

Teaching ”Biological Drugs” in Finnish

Fri, 01 Nov 2024 00:00:00 +0000

In 2022, the steering group of the International Master’s Programme in Pharmaceutical Research, Development and Safety (MPHARM) collectively received the Innoopeli prize 2022 for developing teaching at the Faculty of Pharmacy . As a member of the steering group, I was a bit surprised as none of our students had graduated yet. However, the preliminary laurels received approval earlier this year, when the first batch of the students graduated .

Producing proteins better than the pros

Thu, 31 Oct 2024 00:00:00 +0000

Congratulations, Laura & Akseli! Your article in Scientific Reports ( https://doi.org/10.1038/s41598-024-77104-3 ) is a solid piece of work that has not only relevance for cardiovascular diseases but also for the work that we are doing on lipedema/lipoedema (and therefore, potentially even for lymphedema, which has been the main focus of our research in the past). There are astonishing similarities between coronary artery disease and lipedema, because both can be regarded as lipid storage disorders.And thanks to Khushbu and Betül for helping Laura produce and purify such a high-quality LCAT protein that worked better than the protein preps that are commercially available! Perhaps much of the secret was the high expression levels that we could reach compared to other systems. For the first time, we tried out HEK293T cells with a custom CHO vector ( pCHOKE-B-LCAT-H6 ), and it worked surprisingly well. pCHOKE-B was assembled from scratch and we incorporated several advancements made over the years compared to regular CHO expression vectors. The vector contains

Ouriginal fails more often than not to detect plagiarism

Thu, 23 May 2024 00:00:00 +0000

Ouriginal , the plagiarism detection service formerly known as Urkund, has been in use at the University of Helsinki for a very long time. Because of Ouriginal’s inability to process some of our students’ Master’s thesis, I spent a little bit of time investigating Ouriginal and its problems. Here’s what I found out. From Swedisch to European to US-AmericanIt is unclear to me which software we are really using since Ouriginal is a merger of the Swedish Urkund and the German PlagScan, and in 2021 Ouriginal was acquired by the American Turnitin . I don’t need any of such software, but our university mandates that theses must be scanned by the software. Since I read and evaluate an increasing number of theses every year, I also increasingly use Ouriginal. Ouriginal supports many document formats, but support is buggy Looking at the history of submissions, I realized that until about mid-May 2024, all submitted PDFs had been dutifully analyzed. But last week, something changed since about half of the submitted documents were not processed. The usual tricks (submitting in another format such as .docx, .odt, .ps, .rtf) did work for some, but not all of the theses. One thesis was especially stubborn, and neither our “experts” nor the Original helpdesk staff had any clue why their software could not process it (which makes me again wonder what software their backend is actually using). Ouriginal is investigating already for a month without getting back to me with answers… Our university receives funding from the Ministry of Education based on graduating students, and we lose thousands of Euros for each student who fails to graduate on time. Fee-liable students also have a strong incentive to graduate on time in order to avoid additional costs. Therefore, every delay in the graduation schedule is unacceptable. Ouriginal’s performance disappoints with a shocking detection rate Since there are dozens of ways how to turn a Word document into a PDF, I tried to isolate the problem by submitting test documents to the Ouriginal service. I used manuscripts that we had published over the last few years. I was shocked when I realized that Ouriginal failed to detect plagiarism in more than half of all cases. Paywalls are not to blame since almost all our publications are freely available. Neither the novelty of the publication nor the quality of the journal made a perceivable difference. However, it seems evident that Ouriginal has more problems with non-English documents. It is very difficult to explain why so many freely available scientific texts from reputable journals ( Scientific Reports , Angiogenesis , Annals of Anatomy ) are not indexed by Ouriginal. Failure to detect plagiarism from Helsinki University’s own thesis repository Original does not even index our own university’s freely available PhD theses ( https://ethesis.helsinki.fi ). None of the PhD thesis written in my own lab was recognized. I also checked my own PhD thesis , and it was the only one that was recognized (Ouriginal found it on docslib.org , not our own university’s official thesis repository). Does it make any sense to pay for such an imperfect service? I don’t think so. The omission of freely available texts from important journals seems inexcusable since a simple Google search does a better job. I did Google searches for sentences from the unrecognized texts, and in most cases, Google identified the original source without problems. A Python script to split texts into sentences for individual Google searches and to aggregate the results can be written by any programmer in an afternoon. Why would you maintain your own database if Google does a better job than you can? Plagiarism to the following published manuscripts/theses/proceedings was NOT detected:*

Admission interview

Thu, 09 May 2024 00:00:00 +0000

An increasing number of MSc study programs at our university are incorporating an interview into the admission procedure. Tiina Immonen from the TRANSMED program was the pioneer at the University of Helsinki who ventured first into this territory. If you are invited to an interview at the University of Helsinki, you have already taken the biggest hurdle, which is the evaluation of your application. To be accepted, you have to make sure not to screw up the interview. You don’t need to be stellar, but you need to meet expectations. The reason is that interviews are notoriously tricky to evaluate, and therefore, many programs use them primarily to screen for red flags.

MPHARM milestone

Fri, 26 Apr 2024 00:00:00 +0000

Helsinki University’s International Master’s Programme in Pharmaceutical Research, Development and Safety (MPHARM) is close to another milestone: Our first graduates are soon to submit their theses. On Thursday, we were celebrating after the MSc Theses seminar, where the first batch of students presented the results of their thesis work. At the center is Leena , our benevolent director. Not in the picture is Tomi , who deserves much of the credit for making the Drug Design and Pharmacology track such a success!

Mia Sivén, the world's first professor of sustainable pharmacy

Fri, 05 Apr 2024 00:00:00 +0000

When we were asking our foreign students what made them join the University of Helsinki, several of them mentioned sustainability aspects. Many of the research groups at the Faculty of Pharmacy study topics that are highly relevant to a sustainable future. For example, tackling the increasing threat of antibiotic resistance is a high priority for our faculty. And my group works on the planet’s most environmentally friendly protein production system. There is no part of a drug’s life cycle that could not be approached from a sustainability angle. Therefore, it was high time that this over-arching theme was finally acknowledged by establishing a dedicated professor position. To our knowledge, next month Mia Sivén will start her job as the world’s first professor of sustainable pharmacy . You are probably not surprised that I am very happy about this appointment.

Finished with Finnish?

Sat, 30 Mar 2024 00:00:00 +0000

In her opinion piece in Helsingin Sanomat , Annikka Mutanen picked up on the predicted population decline in the numbers of Finnish people : At the end of this century, the number of people in Finland with Finnish roots will have fallen below 2 million. I won’t be around anymore to experience this, but my children have a good chance to.

Overstretched IT support

Fri, 23 Feb 2024 00:00:00 +0000

The problem: Crash during boot

More than a year ago, a few weeks after receiving my new work computer, it failed to reboot after a system update and got stuck early in the boot process. I soon realised I could still start the computer using “safe mode”. Strangely, nothing seems to be wrong because when I manually exit safe mode at the end of the boot process, the computer works fine. Our IT department has tried to fix the problem many times without success. I even had to work without a computer for about 3 weeks while it was “under repair”. You probably know how much work you can get done without a computer: close to zero.My computer runs Cubbli 20.04.06LTS, an unofficial Ubuntu spin maintained by the University of Helsinki for internal use. Although you can do bioinformatics on a Windows or macOS computer, Linux is hands-down the first choice. Many bioinformatics developers don’t even bother to release their software for Windows. MacOS works mostly fine (since it is also UNIX-compliant OS), but I would have to pay twice the price for the same calculating power.The computer is a Lenovo P350 with an NVIDIA T1000 graphics card, which I use to address two screens. I mainly need the graphics card for 3D modelling, phylogenetics analysis and similar tasks. This graphics card may have caused the trouble. I initially did not want to buy this model, but since there was a shortage of graphic cards at the time, IT convinced me to swap out my original choice against the T1000.

Back to the monograph?

Thu, 01 Feb 2024 00:00:00 +0000

Finland had become internationally known for producing highly qualified PhD graduates in the STEM fields. This was a result of the requirement to publish 4 to 5 scientific manuscripts in renowned scientific journals. Not surprisingly, it took, on average, about seven years to accomplish that feat. Today, Finnish PhD graduates are perhaps internationally more known for being relatively old once they graduate. I myself was 34 years old when I received my doctoral hat . It took me a bit less than six years.On the other hand, my supervisor was so smart to let me do what I wanted, and I spent quite a bit of time with side projects that did not really advance me on my trajectory towards the degree certificate. However, it also meant that I acquired skills, knowledge, and connections that I otherwise would not have. If you take the 10000-hours-rule literally, 10000 hours equal pretty much a six-year PhD education.At the moment, the Finnish Ministry of Education wants to lower the time required for achieving the PhD goal down to 3 years. This article in World University News is to date the most extensive English information piece that has surfaced about this project.My questions are: Why? and How? The why is pretty obvious: Finland has fallen behind in the OECD statistics of highly educated professionals. To polish these numbers, Finland needs more PhD graduates. And since attention-span-reduced politicians cannot be expected to wait six years, it is only logical that they would agree to spend money to increase the degree numbers, provided this would happen fast.But what about the how? How can PhD students learn in 3 years what they normally used to learn in 6 years? If that were possible, it would mean our current PhD education is massively inefficient. Can we squeeze it down to three years without compromising quality? There is clearly an opportunity for optimization. Especially when it comes to the funding of the studies. There has been a constant lack of university-salaried PhD positions. As a consequence, many PhD students spend a significant chunk of their time applying for grants or - even worse - working part-time in order to make ends meet. However, while absolutely a step in the right direction, paying a salary will not cut down the required time by 50%.There is something annoying about science that politicians might not fully understand: It is impossible to predict the outcome of scientific experiments. This very fact is the only reason you do them in the first place! However, if you cannot predict the outcome of experiments, you cannot predict how long it’ll take to get the work done and publish the results. In order to straight-jacket the process of obtaining a PhD degree into a three-year predictable journey, we need to dig deeply into our academic bag of tricks and resurrect the “monograph”. The monograph is an alternative way to attain a PhD degree. Although alive on paper, it had practically died in the STEM fields decades ago, with more than 99% of all STEM PhD theses being publication-based. In some fields and faculties, the monograph has held on to a higher share, but its popularity has been diminishing everywhere for very good reasons. But now it is back!With the monograph, you don’t open up your scientific output to the scientific community for peer review, improvement, and appreciation (in the form of citations). Instead, you write up your research results in a hundreds of pages thick manuscript that is only scrutinized by your supervisors and two external experts appointed by the faculty council. What could possibly go wrong? I hope that I am wrong, but a three-year PhD education will likely not be able to offer the same as a six-year PhD education. Besides, there are other factors that unnecessarily slow down PhD education, which are not addressed in the current pilot. The most notably ignored factor is the supervisor-to-student ratio. Due to the sustained relative decrease in the funding of the basic university functions, teachers and supervisors at Finnish universities are already very thinly stretched, and the current “suboptimal” supervisor-to-student ratio will deteriorate with 1000 additional PhD students who will enter Finish universities over the next year. I fully understand the desire to harmonize the PhD degree at the European level (something that we have done more-or-less successfully with the BSc and MSc degrees starting with the Bologna process in 1999). We don’t know many of the implementation details for this pilot yet. But very clearly, most of the real stakeholders were never asked when this pilot had been cooked up.UPDATEThere have been two articles in the Finnish daily newspaper “Helsingin Sanomat” about this pilot that talk about the two most important points of criticism that have been targeted at the 1000-PhD-students project, namely the decrease in PhD education quality that seems to be inevitable and the very unequal distribution of the funding between different disciplines: https://www.hs.fi/politiikka/art-2000010217525.html https://www.hs.fi/kaupunki/art-2000010242698.html UPDATEThe University of Helsinki has finally posted some information about the upcoming call. The page is not available from the news feed, but you have to know what you are looking for in order to find it. This his is counterproductive given the fact that the application period is only two weeks: https://www.helsinki.fi/en/research/doctoral-school/doctoral-education-pilot

Why you should not use BioRender

Wed, 17 Jan 2024 00:00:00 +0000

About two years ago, our university started subscribing to an institutional plan for BioRender . BioRender is a browser-based scientific illustration software with a large library of pre-made items, including complex illustrations. It allows you to illustrate scientific concepts quickly or to make flow charts for your experimental setups. And given how easy it is to use, the results look rather slick. It’s like the McDonald’s of scientific illustration. It’s fast and gets the job done. Sure, the food in a 3-star Michelin restaurant tastes much better, but most of us rarely can afford that luxury.Why should you not use it despite all of the advantages mentioned above?

Bio-Rad fixes our NGC

Wed, 20 Sep 2023 00:00:00 +0000

UPDATE (situation Dec. 21st, 2024)

We just survived our protein purification course (DPDR-305, see also my other blog posts related to teaching . After having done about 25 runs with the “repaired” Bio-Rad NGC, I sadly have to conclude that the most significant issue remains: that the FPLC becomes unresponsive to commands issued manually. Also, the randomness of these disconnects persisted. Only one student group had problems, but we had several incidents during that single day. That, sadly, concludes our short stint into Bio-Rad territory for protein purification. All of this indicates that any further investments into this device will be wasted time and money. We have neither too much time nor too much money. If Bio-Rad wants to do anything from their own initiative, I am happy to let them do whatever it takes to get the machine into a usable state, but we won’t actively pursue any further actions.The best way to keep your FPLC device in good shape is to have a maintenance contract. Although we have been able to get money from our university to buy a top-of-the-line FPLC twice in the last 30 years, getting money for a service contract is much more difficult. One of the many reasons is that most grant periods are shorter than service contracts, which only make sense if you make them over several years.

Helsinki University dropped from top 100

Sun, 27 Aug 2023 00:00:00 +0000

The largest Scandinavian daily, Helsingin Sanomat, reported the last week that the University of Helsinki had dropped from the top 100 universities in the Shanghai ranking . Now several Finnish academicians have responded . The take-home message of the response could be summarized as *Don’t take these rankings seriously!*Are these rankings really a meaningless indicator of university quality, just a part of the “attention economy”? This is certainly true for those rankings that are not completely transparent about how the ranking procedure works. And for those that are opening up their methodology completely, Goodhart’s Law still applies: When a measure becomes a target, it ceases to be a good measure. Everything is good then, despite Helsinki University’s downfall from the upper echelons of academic research, right? Perhaps not. The many university rankings ( Shanghai , THE , and QS being perhaps the most influential) are just one of many targets that Finnish universities aim at. Another - and perhaps a practically much more important one - is the scheme according to which the Finnish Ministry of Education distributes money among Finnish universities. This scheme might be the secret driver behind the decline of Helsinki University. Under the Sipilä government (2015-2019), the distribution criteria were changed so that the number of produced degrees increased in importance while scientific research (as measured by publication output) became less important. Helsinki University is very research-focused. As a matter of fact, after the changes to the money distribution scheme, Helsinki University’s research output reaches the maximum yearly points that can be given typically at the end of the summer. All publications after that until the end of the year do not improve Helsinki University’s standing compared to the other domestic universities. In Finland, the money from the ministry is very important since they do not operate on multi-billion-dollar endowments as most large US universities do. The HS article specifically mentions that these rankings are not a good way to measure the quality of teaching and, thus, should not influence students’ decisions about where to study. However, some rankings do have meaningful metrics. For instance, the THE ranking compares the ratio between students and teachers. Obviously, if a university does not have enough teachers, it will not be able to deliver good teaching. Bad teaching is neither good for students nor the NYT ranking. I agree that some rankings include questionable practices, such as asking more-or-less randomly selected scientists about what universities they think are the best in their fields. I myself have been contributing to such a ranking in 2021. I tried to skew the needle in favour of Finland and Germany as much as I ethically could justify to myself. Although flawed, I would not completely dismiss rankings. The HS article concludes with a similar sentiment: that the displacement of Helsinki University from the top 100 should be a warning sign to the present government to finally put Finnish Universities on equal grounds with the other Scandinavian (Swedish, Danish and Norwegian) universities which have not suffered from nearly two decades of declining funding. However, this warning sign comes very late, although the decline has been obvious for quite some time for those following university news. The funding situation has already resulted in irreversible losses of human capital. When the purchase-power-adjusted funding for the University of Helsinki went down for the first time, everybody knew that it would take many years before the effects of the funding cuts would become blatantly evident. It finally happened, with a delay of more than ten years. Thanks to all the politicians that have contributed since 2005 by not doing anything, doing not enough or even actively supporting the dismantlement of Finnish academic research. 2005 was the year when I realized that university funding had declined for the first time in real terms.

Bicycle parking on the Viikki campus

Mon, 31 Jul 2023 00:00:00 +0000

We have new bicycle storage spaces in Viikki, about 400 of them. While this sound good at first, let’s look at the details:The access-controlled parking spaces are subject to a fee. I assume it is still “allowed” to park your bicycle outside these access-controlled spaces. However, the Flamma text seems to implicate that all parking on campus areas requires a permit: “There is a fee for parking on all Helsinki campuses.” ( https://flamma.helsinki.fi/en/group/tilat/pyoraily-pysakointi-ja-julkinen-liikenne ). This could have been written a bit more clearly, but I guess the writer had (only?) cars in mind.The Flamma article claims that 36 free-to-use bicycle racks were also installed in the non-heated, outside space in the underpass behind Biocenter 2 (which used to be the gathering space for electric and electronic waste). Yes, but that possibility existed before and has been used before. It’s right next to the smallest (48-rack) access-controlled parking space, the only one where I finally spotted a bicycle. Using the access-controlled parking makes sense if you have an expensive bicycle. If you do, you likely don’t care about the yearly 30€ fee either: expensive bicycle parking for the rich. You pay for your parking via an app. I installed the app on my phone but did not pay the 30€/year fee. Why not? I have two issues with the fee:

Congratulations, Dr. Khushbu Rauniyar!

Sat, 10 Jun 2023 00:00:00 +0000

Defending a PhD thesis is a BIG thing in Finland, and you just did it. Unlike the rest of the world (perhaps except for Sweden), no other country requires as much demonstration of perseverance from PhD candidates as Finland does. On average, it takes four publications and 7 years. The long duration and the lack of well-defined requirements are two problems the Finnish Ministry of Education wants to address over the next few years to level the playing field for Finnish PhD graduates in the international job market. Completing a PhD in Finland takes a lot of Sisu. Sisu is a Finnish word which cannot be translated into any other language, but the recent movie with the same title can give you an idea. Wikipedia defines Sisu as extraordinary determination in the face of extreme adversity .In the “old times”, drugs were discovered based on their effects while not knowing their mechanism of action. This paradigm is more and more turned on its head. Researchers try to understand the mechanism that leads to disease before they start developing or finding a drug. Much of Khushbu’s thesis is about better understanding the mechanisms that govern the action of the primary lymphangiogenic growth factor VEGF-C: The evolutionary origin, activation, and potential as a drug target . Prof. Eckhard Lammert did a great job as the opponent, and Prof. Kari Keinänen did the same as the custos. Dear Khushbu , we wish you all the best for your next big project!

Cutting-edge vascular biology continues at the Wihuri Research Institute

Wed, 10 May 2023 00:00:00 +0000

Taija Mäkinen has been appointed to become the Wihuri Research Institute (WRI) Director starting in 2024. Like the current director Kari Alitalo , Taija has outstanding expertise in lymphatic vascular biology. Taija is currently doing research in Sweden at Uppsala University . With her contributions, she has revolutionized our understanding of how lymphatic vessels form and grow ( 10.1016/j.celrep.2015.02.026 , 10.1161/CIRCRESAHA.116.306170 ).The Wihuri Research Institute , located at Biomedicum Helsinki, was founded and is funded by the Jenny and Antti Wihuri Foundation . It focuses on cardiovascular and vascular biology. This research is essential for the development of new treatments for heart disease. However, blood and lymphatic vessels penetrate nearly all body organs and play a role in almost all diseases, including inflammatory and infectious diseases, neurodegenerative diseases, cancer, and vascular malformations or hypoplasia. Therefore, the research done at the WRI opens avenues for treating many diseases beyond heart disease. The Board of Trustees of the Jenny and Antti Wihuri Foundation has made an excellent choice, even though I am biased for many reasons. I do similar research, and I worked in the same lab as Taija during our Ph.D. education. Unnecessary to mention that Taija graduated faster than I did …

Bad vibes from the new tram

Sat, 01 Apr 2023 00:00:00 +0000

Our showers were banned from use due to the new tram line running in front of my workplace, the Helsinki University Viikki campus. During the trial runs of the tram, I noticed cracks in the changing room’s wall and the showers. I reported these cracks sometime in February to our janitors. Apparently, the structural damage includes the wastewater pipes, and that’s why we can’t have showers anymore. That is a bummer, especially in the summer. To my understanding, the condition of the university buildings had been documented before the construction of the tram line started. Now the investigation is underway to determine whether the additional damage was caused by the construction or the trial runs (and who has to pay for the damage repair).Since I either cycle or run to work, I need to take a shower every morning. My morning routine has become more difficult since the replacement showers have no place where I can hang my wet clothes and towel for drying. While this causes some inconvenience, there will be more serious consequences if there is a causal connection to the tram operation: The university has expensive research equipment, which is sensitive to vibrations. It is incomprehensible how the top university administration could have agreed with the city of Helsinki to run the tram line directly in front of the University building. In fact, the tram now makes a detour to go along Viikinkaari. The more natural and shorter route would have been about 200 meters South of the current track (along Viikintie), avoiding all this trouble. In order to build the tracks directly in front of Biocenter 1 and 2, millions of additional Euros were wasted on vibration-dampening elements to protect our high-end equipment from vibrations. And perhaps all that money was wasted if it should appear that the efforts were insufficient.

Innoopeli Prize 2022

Wed, 21 Dec 2022 00:00:00 +0000

We - the steering group of the International Master’s Programme in Pharmaceutical Research, Development and Safety - received the Innoopeli Prize 2022 !The Innoopeli Prize is given for a significant contribution to teaching in our Faculty. Although biased, I think the award is well justified since we offer many new courses, update existing courses, and translate courses from Finnish into English. It’s been heavy lifting, but we can already see some results in the form of really smart and engaged students, which we managed to recruit!From our programme director Leena Hanski: “In January 2021, we started the work as a steering group, with no learning objectives, curriculum, admission criteria, or even website, not to mention a single decision on practical arrangements for running the programme. We still have plenty of work in front of us, but I am convinced we can keep up the pace and make this programme a great place to polish the future stars of pharmaceutical research, development and safety. Our first set of students has been a great source of inspiration and motivation for many of us, and I also want to specifically thank them for their openness and willingness to share their stories, thoughts and expectations.”

Bioactive VEGF-C from E. coli without in-vitro folding!

Fri, 28 Oct 2022 00:00:00 +0000

Our article Bioactive VEGF-C from E. coli has been published in Scientific Reports. Read here: https://doi.org/10.1038/s41598-022-22960-0.As a matter of fact, I did the first experiments expressing VEGF-C in E. coli in 1999, but never got active protein. In the following 15+ years, we exclusively used eukaryotic cells (yeast, S2/Sf9/Hi5 insect cells, CHO) to produce VEGF-C. We reactivated the “VEGF-C in E. coli” project a few years back and we finally reached our goal last year. However, it was much more work than we originally anticipated. In the beginning, all attempts went South, and to rescue the project, we developed an in-vitro folding protocol. It was perhaps more luck than ability that we stumbled upon a combination of solubility tag and redox-modified E. coli strain that can pull off the trick to produce directly bioactive VEGF-C without the need for an in-vitro folding step. We decided to include also our unsuccessful attempts (CyDisCo and periplasmic expression) in the results section to avoid the file drawer effect.

The eLabFTW electronic lab journal: ready for prime time?

Fri, 03 Jun 2022 00:00:00 +0000

Some love it and some hate it: the electronic lab journal (ELN). Already a decade ago, the prediction was that in 10 years the paper lab notebook would be a thing of the past. In reality, the majority of academic labs are still using paper in 2022. The transition has not been helped by literally hundreds of commercial offerings that are all mutually incompatible. We started to experiment with ELNs in 2013, testing a few commercial and open source solutions. The worst of the pack did not even allow us to test drive them before buying (e.g. LabVantage seems to think you won’t buy once you have tried it, and they are spot-on!). We settled on eLabFTW , an open-source project with the main development happening at the Institute Curie in Paris, France. It’s a web application built with PHP and MySQL. There is also a peer-reviewed publication describing it: https://doi.org/10.21105/joss.00146 and a general Nature Protocols review article, that discusses ELN implementation: https://doi.org/10.1038/s41596-021-00645-8 .Deployment for teaching at University of HelsinkiWith the recent update to version 4.3 , the final hurdle for large scale deployment has been taken. Everybody with a helsinki.fi account can now log into the system with university account credentials. This makes the onboarding of many new users much easier. I am planning to use the system for our new course “Recombinant DNA technology and genetic engineering”. At the moment, the server is only reachable from inside the university network. If you want to use it from home, you need to use a VPN. Over the years we have been accruing about 25 users, and it will be interesting to see how the system performs when the user numbers will double or quadruple. The system runs in a docker container on an Ubuntu 20.04 LTS virtual server, which we, unfortunately, cannot upgrade or extend without additional financial support. So if you are interested to use an ELN, secure your spot today by logging into https://elab.ltdk.helsinki.fi , using the “Login through your institution” option on the bottom. You will have the option to choose a team. The team administrator needs to approve you before you can use the system. If you cannot find your lab among the teams, it means that you are the first user from your lab using this system. In that case, you should choose the team “Helsinki University” and contact me via email ( michael@jeltsch.org ), because I will need to register a new team for your lab, and you will be the administrator of this new team.Access for visitorsIf you do not have a University of Helsinki account, you can still use the system if you are inside the Helsinki University Eduroam network, but you will need to use the “Register now” link, and your account needs to be approved by a system administrator.Running it on your local machineThe system requirements of eLabFTW are fairly low, and your laptop is likely to have no problems running a local copy of the docker container. While installing eLabFTW on a recent Windows or macOS computer is possible, it is somehow counter-productive as it does not provide network accessiblity and team functionality. Even if you don’t need any of that, I would suggest that you repurpose an old desktop computer for this task and run it on a regular Linux server installation. I am happy to answer all possible questions that you might have (from a system administrator’s and end-user’s perspective).

PhD thesis defense about hepsin's role in breast cancer

Sun, 24 Apr 2022 00:00:00 +0000

Last Saturday, Denis Belitškin defended his Ph.D. thesis. The topic was The role of type II serine protease hepsin in breast cancer signaling . I thoroughly enjoyed the discussion with the opponent Karin List , which happened over Zoom with only a small real-life audience. Proteases have slowly become one of my favorite protein classes. In the old days, they mostly were appreciated for their degradation function, but it is meanwhile clear that they are much more complex. My own interest is their role in the activation of signaling molecules. In this context, proteases are signaling molecules, playing at the same level as hormones, cytokines, and growth factors. Thanks, Denis for a convincing performance and the karonkka!

University helpdesk recommends Zotero, but does not provide meaningful support

Sun, 20 Mar 2022 00:00:00 +0000

With the end of last year (31.12.2021), the University of Helsinki discontinued licensing its default bibliographic software tool RefWorks . Strangely, you cannot license RefWorks as an individual. That means when your academic affiliation ends, there is no way for you to continue using the software. Perhaps, the current owner of RefWorks (Clarivate) will kill it completely because RefWorks is a direct competitor of Endnote , which is the reference management solution that Clarivate is focussing on, given Endnote’s integration with Publons and the Web of Science (WoS), which is best known for its Impact Factor . Not coincidentally, Clavivate is owned by Thomson Reuters, which is the company that litigated against Zotero for offering its users the possibility to convert proprietary EndNote citation style sheets into the interoperable and standard CSL format . The recommended replacement for RefWorks is Zotero . I have no problem with this since I like Zotero and have been using it as my default bibliography management tool for now more than 10 years. On top of the fact that it is free, it combines two important features, which make it unique and superior to commercial solutions:

Meet the teacher!

Fri, 31 Dec 2021 00:00:00 +0000

Almost 30 years after starting my academic career, I started to teach at the Faculty of Pharmacy (without much pedagogic experience and education). Mostly, I teach stuff that I have real-life research experience and expertise with: Recombinant DNA technology, genetic engineering, protein production and purification, and - most notably - protein drugs. Following the University of Helsinki motto Researchers teach, teachers research . Despite my lack of experience, I was part of the Helsinki University “Meet the teacher!” feature, which is aiming at the prospective International Master’s students: https://www.facebook.com/HelsinkiUniversity/posts/10160122296028083

Language boost

Fri, 17 Dec 2021 00:00:00 +0000

I am having a new attempt at learning Finnish! Until very recently, my career has progressed in Meilahti at the Faculty of Medicine, University of Helsinki. After the Research Fellow period financed by the Academy of Finland, my career prospects at Meilahti were meager at best, as almost all vacancies require good Finnish or Swedish language skills. In Finnish medical schools - unlike in many other study programs - you have to be able to teach in Finnish or Swedish. In other EU countries, there are many universities where you can study medicine without knowing a word of the local language, but Finland does not (yet) recruit foreign students for medical degrees.Before I started to study at the university, I was already once in similar language trouble. In the autumn of 1989, when the political changes in Eastern Europe made free travel possible, I decided to visit Hungary. My interest in Hungary originated from several Hungarian friends of mine, who were living in exile in former West Germany. When I arrived in Hungary in the spring of 1990, I did not speak a single word Hungarian. However, none of my Hungarian friends ever spoke anything to me but Hungarian. I remember with particular fondness Tomi and Timea and all their family and friends who patiently listened to my ramblings and corrected grammatical errors in my speech. Learning Finnish in Finland is different. Why does nobody want to put up with my bad Finnish? I have come across the idea that Finnish people are not used to foreign accents. I don’t subscribe to this explanation. The former Eastern European countries were at the time also isolated and linguistically homogeneous - in much the same way as Finland. Is it perhaps because nowadays nobody seems to have time for anything? In the autumn semester, I took part in a Finnish language course offered by the University of Helsinki. The course was part of the language boost (kielibuusti) project. Studying languages takes time. We always wonder how young children are so good at learning languages, but we forget that they are learning full-time. The Finnish language course has certainly affected my other work, and for this reason, I fully understand those foreign researchers who do not even waste a single second learning Finnish.As far as learning Finnish is concerned, I think the problem is not so much with the course offerings, although they could be better. The problem is rather that you don’t get to exercise your Finnish in real life because there is always someone around who - for very good reasons - doesn’t know Finnish or doesn’t want to learn it. In my own lab, all the native languages of the lab members - including Finnish - are minority languages. And without exception, all the people I talk to speak excellent English. It takes real effort to use any other language than English (that also applies to my own mother tongue, German). One of the goals of the Language Boost course was to get ourselves a language buddy, someone with whom we could communicate regularly in Finnish. After half a year, I am still without a language buddy. Although the teachers on the course were excellent, two hours of Finnish a week is unfortunately not enough.I know several researchers who have come to Finland from abroad and who speak excellent Finnish. However, most of them have family ties to Finland. Therefore, they have had to deal with Finns who do not speak English. They were forced to learn to speak Finnish. The same thing happened to me in Hungary 30 years ago: most people did not learn English at school. We had only one language of communication, and I used it all day long in all situations.This post was inspired by Reetta Vairimaa's article "Claudia and Celia" in the magazine Yliopistolainen (1/2018), which unfortunately is not available online.``Here is another aspect of the problem: There is simply not enough time to study Finnish for most foreign researchers. Compared to their native counterparts, they have already a higher workload even without learning Finnish. Building up a network - both professionally and privately - is lots of work. The numbers of Finnish learners at universities (20-30%) that were mentioned in this Acatiimi article ([Too few people study Finnish or Swedish](https://acatiimi.fi/2022/02/07/too-few-people-study-finnish-or-swedish/)) sound very high to me. I know lots of foreign researchers but very few of them have substantial knowledge of Finnish (but perhaps that is only true for Ph.D. students, which are overrepresented in my distorted view).

Kilometrikisa

Fri, 08 Oct 2021 00:00:00 +0000

Kilometrikisa (“kilometre competition”) is a cycling competition for workplaces, which aims to encourage bicycle commuting and cycling in general. Team members record their daily cycled distance on the website https://www.kilometrikisa.fi and the team with the most kilometers wins. Additional prizes are raffled between all participants (I actually for the first time got lucky this year and won a free massage at UniSport ).There is a summer competition, running from May to September, and a winter competition (“talvikilometrikisa”), running mostly throughout January and February. Do not ask me why there are no spring and autumn events. I have been riding throughout all year for the last decade, with the exception of winter 2012/2013, because I broke my leg when cycling home from work. For me, October, November and December as as good cycling months as January and February. Actually they are better because due to global warming they tend to be snow-free in the recent years. If you commute early in the morning, before the snowplough has removed 30 cm of fresh snow, you know that you will get stuck many times, even with the 57-622 Schwalbe Ice Spiker Pro tires.My performance in this competition has collapsed since my lab moved from Biomedicum in Meilahti to the Biocenter 2 in Viikki, because my commute has shrunk from 14 km/day down to a meager 4.5 km/day. I still score very high on the list when it comes to the number of cycling days (109 for the last season), but according to the cycled distance, I am just slightly above average (place 58 with 1031 km). Our team (“Helsingin Yliopisto”, University of Helsinki) placed 143th this year in the competition for big workplaces.I am always wondering whether the total amount of cycled kilometres and the number of participants are increasing over the years, which should be the case if we are serious about combatting global warming. The first kilometrikisa event was held in 2014, so there is enough data to see trends. Unfortunately, the website does not give this information. It would be possible to scrape it and calculate it from the individual results, but I have enough other things to do atm. Maybe sometime in the future.

How attractive is Finland for international students?

Sun, 29 Aug 2021 00:00:00 +0000

One apology upfront: All the links in this post are to Finnish sites, demonstrating one of the problems that foreign students face in Finland: a language that doesn’t resemble any other European language (apart from Estonian and Hungarian, which also belong to Finno-Ugric language family ).Foreign students are generally having a good time in Finland. Although not everything is perfect, the University of Helsinki (and Finland in general) is worth considering when you want to study abroad. This is the bottom line from a feedback survey among more than 800 international students from the years 2020 and 2021. Especially the high quality of the teaching was appreciated. Other points in which Helsinki University excelled were the safe environment and the handling of the Covid-19 pandemic.However, the latter has also a downside, as more encounters and discussions with the academic staff were on the wish list of the students as well as more social support. This is hardly surprising given that international students cannot fall back on the same networks as the locals when they arrive in the country. The worst single issue appeared to be the reception of the students. Arriving and dealing with an unknown and incomprehensible bureaucracy is often too much for newcomers. Discrimination was only experienced by 4% of the respondents and among them, language discrimination and loneliness were the most common.I always warn students who tell me that they plan to apply to the University of Helsinki. You want an honest opinion on whether to start your studies in Finland? Ok: It can get pretty cold and it will get REALLY dark in the winter. However, Helsinki is still one of the more livable places when it comes to the cold and dark season. It rarely gets below 0°F (-17.8°C), and being on the South coast it’s also one of the least dark places. And global warming is doing its best to increase the temperatures. Finland is already the insider’s bet for long-term real estate investments: still cheap enough, but with extreme growth potential once climate change converts Southern Europe into a smelting furnace. However, these scenarios will fully realize only the current political decision-makers have already kicked the bucket. But if you are in for the long haul, Finland might be THE place to be. But again, if the gulf stream collapses, you’ll be thrown back to square one. Thank your parents for the mess they have left you ( https://www.theguardian.com/environment/2021/aug/05/climate-crisis-scientists-spot-warning-signs-of-gulf-stream-collapse ).Unfortunately, as good as Finland might be for studying, staying in Finland for good is a different story. Even though Finland needs to boost immigration to make up for its declining and aging population, there are still unfortunately too many hurdles to overcome before settling down becomes a realistic option for most foreigners. The language is only one of them, others being mentioned in a recent article in the largest Finnish daily newspaper (Helsingin Sanomat) are the difficulty to become integrated into the Finnish society, the for foreigners incomprehensible bureaucracy, and the low salary levels. But also growing resentments towards foreigners within the Finnish population, manifested in the success of the “Finns Party” (formerly known as “True Finns”), are not helping. Most other European countries also fight with right-wing political currents. In my home country Germany, the AfD (roughly equivalent to the Finns Party) is not considered by any of the democratic parties as a possible coalition partner (wishful thinking on my part?). But here in Finland, the Finns Party has been already in a coalition government, and only the social democrats and the leftist coalition have a clear “no” position in this matter.Just recently, the newly elected major of Helsinki Juhana Vartiainen commented on the attractivity of the Finnish labor market for foreigners:“A miserable failure on Finland’s part. The political consciousness has been very slow to even grasp that we need labor immigration at all.” ( Helsingin Sanomat, 28.08.2021 ).But all that aside, academic teaching is at a very high level. And it is free for EU/EFTA residents (and holders of qualifying degrees from those countries). For paying students, the tuition fees are a bargain compared to many other universities that play in the same league (between 13000 and 18000 Euros per year, depending on the study program). However, the university staff will have to pay a high price to maintain this quality. For the current decade (2020-2030), the ministry of education has the goal to increase the number of completed university degrees by 100000 ( https://www.acatiimi.fi/4_2021/15.php ). At the same time, the university budget has been cut. The government will probably compensate for the cuts in a media-attraction gathering “rescue the university” move to distract from the fact, that we need dozens of millions on top of this to provide the same high level of teaching for those 100000 additional degrees over the coming years. At the research level, academic staff has been fighting an uphill battle since 2005, when the inflation-adjusted budget for R&D decreased for the first time. But meanwhile, students start to feel the lack of sufficient funding e.g. when their teachers simply do not have anymore the same amount of time for them as they used to.I have no other choice than to advise students against an academic career in general. Most other European countries have similar problems, but perhaps not at the same level as Finland. And the students know that academic funding is especially bad in Finland .

Where to move to from RefWorks?

Thu, 10 Jun 2021 00:00:00 +0000

I never understood why our university pays for proprietary reference management software. Perhaps some old people in the administration still live in the 90s of the last millennium when EndNote was de-facto the only decent reference management software for WYSYWIG text processors. But those times are long gone. Finally, our university is at least dumping one of its proprietary reference managers:

TuKoKe success for our TET interns!

Wed, 09 Jun 2021 00:00:00 +0000

Here in Finland, 8- or 9-graders make a one- or two-week “Introduction to working life” internship at a workplace of their choice ( TET, työelämään tutustumisjakso ). The Covid-19 pandemic has also screwed this one thoroughly up, but our lab did manage to host a few interns when the Covid-19 numbers were pretty low in the autumn.One group, consisting of Pessi Bask, Rasmus Pouta and Okko Siljander from the Käpylä Primary School did study the suitability of run-of-the-mill plastics used for 3D printing for the culture of mammalian cells . Under the supervison of Niklas Koppatz, they entered with this project the TuKoKe nation-wide science- and technology fair and not only won the third price , but also additionally the Aalto University’s Design Factory Award and a stipend from the Finnish Invention Foundation (Keksintösäätiö) for the inventive nature of their work. Congratulations!

Master's Programme in Pharmaceutical Research, Development and Safety

Mon, 12 Apr 2021 00:00:00 +0000

The University of Helsinki is expanding its repertoire by offering a new International Master’s Programme in Pharmaceutical Research, Development and Safety . The year 2020 has shown how immensely important pharmaceutical science is for human societies. And this importance will only grow in the future! Besides emerging novel viruses, there are many challenges in front of us. The list below is just a start…* *

Eduroam installation on Linux

Tue, 23 Feb 2021 00:00:00 +0000

This morning it took me an hour to get Eduroam working. Eduroam is the international WLAN roaming service for university students and staff. I brought in my (non-university managed) laptop to work and tried to get connected. I finally found the instructions on the IT Helpdesk site on place place 19 (from 21 results shown on the first page when searching for “Eduroam Linux”): https://helpdesk.it.helsinki.fi/en/instructions/logging-and-connections/networks/installation-eduroam-network-on-ubuntuAs usual, the instructions are from many years back and no longer work on a “recent” system such as Ubuntu 20.04 LTS. On top of this, I had some old, dysfunctional Eduroam settings lingering around from a previous failed attempt. For the instructions below, you will need the Eduroam configuration tool, which you can download from https://cat.eduroam.org . To make it work, I had to do the following things:

Our first OER (Open Educational Resource)

Wed, 03 Feb 2021 00:00:00 +0000

When I started my new position at the Faculty of Pharmacy, it was clear that I would be going to do more formal teaching than before. Even though I have lectured before, I typically was only modifying a conference presentation in which I presented the research work from our laboratory. However, that does not fly for undergraduate students, and hence I am assembling lectures from scratch. Although there is much hype about Open Science, there are few or no open educational resources for the topics that I know to teach: genetic and protein engineering, protein drugs, biologics. Because I think, that there should be more openly available teaching material, I decided to make my lectures openly available. However, I soon realized that it is very difficult to replace copyrighted material with free alternatives such as public domain or Creative Commons -licensed material. 80% of the images and illustrations are easy to replace, the next 15% take you as much time as the first 80%, and for the last few images it seems impossible to find copyright-unencumbered alternatives. In the end, I generated the lion share of material myself. For this specific lecture, I have not found any usable image of Judah Folkman . Needless to say that if money was not an issue, I could just buy one for a few hundred bucks, but it still would not be possible for others to reuse it. As a temporary solution, I drew an image myself. I am not good at drawing, help me out it if you can!Today, I have finally uploaded my first lecture to the Library of Open Educational Resources : https://aoe.fi/#/materiaali/1212 . It was an introductory lecture to Protein Drug Discovery & Development for BSc students of Pharmacy (course PROV-105), which dates back to September 9th, 2020. The Library of Open educational Resources is maintained by the Finnish Ministry of Education. I also made an entry to Merlot collection (which is perhaps the biggest OER catalog): https://www.merlot.org/merlot/viewMaterial.htm?id=773405613.However , I am not entirely satisfied with the situation, since I prepared the lecture using Google Slides. Why Google slides? Sadly, it is the only functioning real-time collaborative presentation software. Due to this, the original version of the lecture slides is not available from aoe.fi. However, there is a link to the Google Slides. I have obviously included the same presentation in PDF and ODF format after converting it and all the editable source files (mostly in SVG format). And if the collaborative online editing of LibreOffice should finally become usable, we will probably switch to using that instead of Google Slides. The live online version is the more useful resource. In addition to the fact that this is the original version of the slide show, it will be also updated regularly (since I will give this lecture repeatedly), while the uploaded PDF/ODF file will become more and more obsolete over time.UPDATEI have meanwhile managed to upload another lecture to https://aoe.fi . All of my future contributions will be available from my collection page .* *

Editing Zoom recordings of teaching sessions with FFmpeg

Wed, 25 Nov 2020 00:00:00 +0000

Based on student feedback, we have been organizing a new course for the TRANSMED MSc program about drug discovery and development. It is what you call in German a “Schupperkurs”. I never have found a satisfactory translation of this word in English. It means that we just want to raise the students’ interest in this course. If they like it, they can take any of the many in-depth courses that are offered e.g. at the Faculty of Pharmacy , where there will be more teaching in English in the coming years due to the planned International MSc program in Pharmacy.

GeneCellNano Flagship

Wed, 18 Nov 2020 00:00:00 +0000

The GeneCellNano program was selected as an Academy of Finland Flagship. The idea behind the flagship is to make progress in the treatment of important diseases using advanced biologic technologies. Target diseases include ischemic heart disease, selected cancers, and retinopathy. The application was spearheaded by Seppo Ylä-Herttuala from the University of Eastern Finland and Seppo Vainio from the University of Oulu. In addition to groups from these two universities, the consortium features also groups from Aalto University (Olli Ikkala) and the University of Helsinki (groups Marjo Yliperttula, Timo Laaksonen, Hélder A. Santos, Tatu Lajunen, and my own).Link to the Academy of Finland press release: https://www.aka.fi/en/about-us/whats-new/press-releases/20202/academy-of-finland-selects-four-new-finnish-flagships/

Medical research in Finland

Sun, 11 Oct 2020 00:00:00 +0000

Want to become a researcher in Finland? Why not? At the University of Helsinki , there are quite a few professors from German-speaking countries. Increasing the proportion of foreign researchers is an explicit goal of all Finnish universities. As far as the quality of academic research is concerned, Finland ranks in the middle of the pack in Europe. Only one of Finland’s 10 universities ranks among the world’s top 100: the University of Helsinki (74th in the 2020 Shanghai Ranking ). In contrast, four German universities make it onto the list, which is otherwise dominated by Anglo-American institutions (Ludwig Maximilian University of Munich, Technical University of Munich, Heidelberg University, and the University of Bonn, ranked 51st, 54th, 57th, and 87th, respectively). It should be noted, however, that these rankings represent an average across all of a university’s research fields.

University Pedagogy (UP2.2, 2019): Assessment of Learning and Giving Feedback

Fri, 02 Oct 2020 00:00:00 +0000

Becoming a qualified teacher in FinlandThe degree requirements for the 60-credit module in University Pedagogy (UP) consist of 25 credits of basic studies and 35 credits of intermediate studies. Although UP focuses on teaching at the university, the completed module qualifies you also for teaching at schools. The Pedagogy Center of the University of Helsinki organizes the courses of the basic study modules (25 ECTS credits) in English. However, if you want to complete the whole module, you will need to take courses which are only offered in Finnish or Swedish. That means you cannot become a qualified (“pätevä”) teacher without knowing Finnish or Swedish. I do not know whether my Finnish is meanwhile good enough to be able to do that. For the time being I stick to the courses taught in English.**University Pedagogy 2.2 (2019)**In the 2019 autumn term, I took the UP2.2 course (without taking UP2.1 first). We had a very nice teacher (Jokke Häsä), but I still don’t understand why he switched from doing Mathematics to teaching Pedagogy. Certainly a gain for pedagogy since he understands the statistics and we had some interesting forth-and-back about the statistics of the Johnston & Miles paper that we were reading. They paper is also attached to this post and the reporting about their statistical methods leaves much room for interpretation. I actually sent an email to the first author, but she had just retired a few months ago. Although I did not get an failure-of-delivery error, she perhaps did not anymore feel the need to respond.Blind flyingFor me, one of the biggest issues was, that I had nothing to compare too when I was preparing my assignments. When I am writing manuscripts for journals, I have thousands of examples which I can study and to which I can compare. So I decided during the course that I would make all my assignments public. Embarrassment included. But maybe some future participants of UP2.2 will have something to compare to. Sort of an exemplar. Not perfect, but passable. I only post my own assignments.**All my assignments available under CC0 (= no strings attached)**All this stuff is shared under the CC0 : Use it as you wish, no need to acknowledge me. The group assignment is the only thing missing here since I would need to get everybody’s green light, which is not going to happen. I should have done this 9 months ago, but I simply forgot. There was just too much other stuff happening.I did ok in the course, but I still don’t know anythingWhat grade did I get? Our group assignment got a 5 (on the scale of 1 to 5, where 5 is the best grade) and my own stuff a 4. Thanks to all the great members of team Carbonara! That averaged out as a 5 for the whole course. For some strange reason, the Moodle course page still shows that I only completed 66% of the course assignments, but WebOodi shows that I received the credits. So much for the wonders of our IT systems…

Dr. Sawan K. Jha: Mechanism of VEGF-C Activation […]

Mon, 01 Jun 2020 00:00:00 +0000

My first Ph.D. mentee successfully defended his thesis on the topic Mechanism of VEGF-C Activation and Effect on Lymphatic Growth and Regeneration . Due to the COVID-19 situation, we organized the event remotely and used the Zoom virtual meeting software. The opponent was Prof. Jonathan Sleeman from the University of Heidelberg. Both the defendant and the opponent did a fantastic job, and the discussion brought to light several new directions for future research, which I had not been thinking about before. VEGF-C is a tricky protein and I am sure it still holds some surprises for the diligent researcher. Unfortunately, there was no reception, no dinner, and no karonkka (after-dinner graduation party), but we are planning to have a party later this year when the COVID-19 situation permits!

University of Helsinki loses court battle about lawfulness of 2015 mass layoff procedures

Wed, 16 Oct 2019 00:00:00 +0000

In 2015, the University of Helsinki sacked around 370 of its employees (and did not prolong temporary contracts of perhaps as many). Many survived only because their contracts did not end around the time when the “central committee” of the university administration overreacted when they realized how bad the university’s financial situation really had become. About 10 years of conservative financial austerity culminated in the spring 2015-elect government led by Finnish businessman Juha Sipilä, who was jointly responsible for the massive funding cuts that led to the massive layoffs at the end of 2015.Last month, a Finnish district court ruled that the layoffs had not been legal in the sense that the University of Helsinki did not adhere to the Finnish law on several accounts (" Yhteistoimintamenettelylaki ", in English something like “Act on Collaboration in Businesses”). Notably, the court rebuked the university for its information policy and their lack of attempts to negotiate alternatives to the layoffs. This was exactly the feeling of most employees at the time: The central administration had cooked up a “solution” in some backroom meetings without consulting any of the stakeholders, and then it carelessly pushed this solution regardless of the consequences.The compensations that were granted to the plaintiffs were 5000 or 6000€ depending on the length of their employment. One can argue about the pros and cons of the US-American legal view on compensations (which aim at deterrence rather than compensation), but even for a financially challenged University, 64000€ (including 35000€ legal costs and 29000€ compensation to the five plaintiffs) will neither help the plaintiffs very much nor deter any university from repeating such actions. And judging from the response, the university’s central administration does not agree with the view of the district court, that the procedure did not follow the law.The largest Scandinavian daily newspaper Helsingin Sanomat reported about this case: https://www.hs.fi/politiikka/art-2000006245821.html and also many other magazines, e.g. http://www.acatiimi.fi/6_2019/12.php .

Protein Purification Course 2019

Wed, 31 Jul 2019 00:00:00 +0000

We are again hosting the DPBM protein purification course this December in our lab. Secure your place as this practical course is popular and there are only 16 seats. You can bring your own protein and we will individualize the course program based on your needs!More information: http://research.med.helsinki.fi/corefacilities/b3p/teaching.htmlRegistration : https://courses.helsinki.fi/en/dpbm-135/131042336

Apply successfully to the University of Helsinki

Sun, 28 Apr 2019 00:00:00 +0000

What are my chances to be accepted into a Helsinki University Master’s Program?

This differs greatly from year to year and between the different programs. The admission rates for most individual programs have been anywhere between 5% and 40%, with popular programs like Environmental Change and Global Sustainability or Economics at the low end and e.g. Forest Sciences and Theoretical and Computational Methods at the high end.

Mounting group directories via the fstab

Mon, 11 Feb 2019 00:00:00 +0000

At the University of Helsinki, one can apply for group directories, which is simply disk space on a NAS. These are easily mounted when you use a university-managed computer via the university menu, but what about if you use your own machine? At least for Ubuntu Linux, the way to mount these directories has changed multiple times during the years and it again broke recently. The current entry in the /etc/fstab file in my (Vanilla, non-university-managed) Ubuntu 16.04 is as follows:# HY group directories//group2.ad.helsinki.fi/h204 /home/local_username/GROUP-drive cifs noauto,user,user=hy_username,nobrl,uid=1000,gid=1000,file_mode=0666,dir_mode=0777 0 0Then you can simply execute “mount /home/local_username/GROUP-drive” and you will be asked for your HY password. The number 2 and the string “h204” in the server address (group2.ad.helsinki.fi/h204) are specific for the cost center which is in this case H2042 (taking the first digit from the cost center string and first four characters from the cost center string, respectively).And here are some instruction on how to do it manually on a Macintosh:https://helpdesk.it.helsinki.fi/en/instructions/saving-and-sharing/group-storage-space/remote-access-home-and-group-directory-mac

Internationalization in everyday operations at Meilahti campus

Mon, 22 Oct 2018 00:00:00 +0000

Meet the rectors at MeilahtiLast Thursday (18.10.2018), the new rector of Helsinki University Jari Niemelä and the four vice-rectors (Sari Lindblom, Paula Eerola, Hanna Snellman, Tom Böhling) visited the Meilahti campus for an open question and answer event. Hardly any foreigners were present during the event. Consequently, the language of communication was Finnish. Obviously, foreigners won’t participate if they do not understand and speak the language of the event. And since foreigner’s don’t participate, there is no reason to change the language of the event, and so the circle continues… Traditionally Finnish and Swedish onlyThe Meilahti campus holds a special position when it comes to language use since until very recently, it was impossible to receive a degree from Meilahti without knowing Finnish or Swedish since the only degree programs were not offered in English. However, the situation has been changing (e.g. with the move of the Psychology Department to Meilahti and the establishment of new degree programs like TRANSMED ), but old habits die hard. Trailblazers RPU and HiLIFEThe trailblazers for internationalization at the Meilahti campus are the Research Programs Unit and HiLIFE. The postgraduate students and postdocs of the Research Programs Unit (RPU) and the HiLIFE recruitments are the two most internationalized parts of the Meilahti campus and consequently, Hannu Sariola (previous vice dean for research at Meilahti) and Tomi Mäkelä (the HiLIFE director) brought up the topic of internationalization pointing out that the rules of the university allow for more language flexibility than is actually implemented. To date, the only official languages at the University of Helsinki are Finnish and Swedish, although more English-speaking than Swedish-speaking students are enrolled. English is also the de-facto language of almost all scientific endeavors. Balancing the domestic languages with English likely has no perfect solution. If the university wants to optimize its international impact and success, the role of Finnish and Swedish inevitable has to decline unless massively more resources become available.**Separate events?**In order to engage the foreign staff as well, the dean of the faculty recently organized the faculty staff meeting twice: once in English and once in Finnish. I am not sure whether such separation is a long-term good idea, but it addresses the issue pragmatically and gets the job done. If someone suggested separating the faculty X-mas party according to language, that would be considered discriminatory, but for a working meeting, nobody seems to object…**PS:**I am not the only one who is aware that internationalization has a long way to go. There is a nice article on the Helsinki University intranet portraying the new vice rector Hanna Snellman and her take on the issue: https://flamma.helsinki.fi/en/HY377022 . However, the university keeps most of its interesting web content behind locked doors (inside their Flamma service), inaccessible to the general public, who is paying the university’s bills… What does the university fear? More transparency?

Strike at the University of Helsinki

Tue, 27 Feb 2018 00:00:00 +0000

A strike warning has been issued for tomorrow (28.2.) for the University of Helsinki. The reason is that the negotiations about between the employers and employees about the wages and working conditions are stuck and the strike is used as a means to speed up the movement of the employer’s negotiation position towards an acceptable compromise. Business as usual? After all, there hasn’t been a strike at the university for a very long time…While almost everybody agrees that Finland’s future is built on knowledge and innovation, the appreciation of the very people that are generating knowledge and innovation seems to have hit an all-time low if appreciation is reflected by working conditions and payment levels.I guess the underlying cause is not so much the concrete offerings of the employer (or the lack thereof), but the disregard and disrespect for academic education, research, and development that has been growing over the years, accelerated by the 2015-elect government, which refuses to invest into the future. Universities should not behave like companies trying to maximize their profit on the cost of their employees and the quality of their product. With some exceptions , everybody with a little bit of self-respect is participating. All major unions, including the students’ and professors’ union, are supporting this action. Apparently, professors will go on strike for the first time in the history of this country ( https://yle.fi/uutiset/osasto/news/finnish_professors_walk_out_in_first-ever_strike/10095355 ).

Remote desktop sessions to your Helsinki University work computer

Mon, 15 Jan 2018 00:00:00 +0000

If you have a work laptop, you can take it home to do work. But what if you have a desktop computer and need to access it from home? The technology to make this possible exists for more than 20 years, but if you think that University IT has made this easy for you, you would be wrong. In fact, I don’t know anybody who knows how to do this (let alone how to make the process easy). Even with the setup explained below, some things do not work well (e.g. I never could figure out how to get the file sharing to work with a Mac-to-Mac connection and thus I still use Fugu with a separate tunnelled sftp connection to transfer files). You have several options:

Practical Course: Purification and Characterization of Recombinant Proteins (DPBM-135)

Sun, 10 Dec 2017 00:00:00 +0000

Teaching material, results, etc. for the DPBM course “Purification and Characterization of Recombinant Proteins” ( https://courses.helsinki.fi/en/DPBM-135/120171139 ):

Acatiimi article about our lab

Mon, 27 Nov 2017 00:00:00 +0000

However - unlike in the previous story - this time there is a group image, showing who does the real work!

TRANSMED - the most medical research education for your buck

Sat, 25 Nov 2017 00:00:00 +0000

Starting from this autumn term, even Finnish universities, so far the strongholds of free education, have started to demand study fees from students from outside the European Union (EU) and European Economic Area (EEA). Between 13k€ and 18k€ per year, the tuition fees are still modest compared to some other universities. At the moment, compared with other universities, you probably get the best returns for your money at the University of Helsinki .The TRANSMED Master’s Program is perhaps the best example. Given the real costs of a research-oriented medical MSc education in a world class environment, the 15k€ tuition fee per year is a bargain compared to similar programs at other universities. And even better: the chances to be accepted are surprisingly good. Some have proposed to increases the fees, but no concrete plans exist at the moment.So what is keeping foreign students from flocking to Finland? The cold winters cannot be blamed anymore. Thanks to global warming, most of the recent Christmases have been snow-free here in Helsinki. In fact, global warming seems to hit Finland harder than most other countries. Need more reasons to come? Have a look here: http://www.visitfinland.com/article/greatest-things-about-finland/

About the agility of large organizations

Thu, 15 Jun 2017 00:00:00 +0000

A decade for the switchI don’t remember exactly, but the idea to deploy a decent content management system for the entire web presence of the University of Helsinki is probably 10 years old. I had reserved the domain jeltsch.org in May 2003 (after I had completed my PhD) to host my private web site. The oldest snapshot of my web site on the internet archive dates back to December of the same year. Like the Helsinki University IT staff, I realized that updating a web site by updating individual html pages is very time-consuming. In 2006, I was - exactly like the University of Helsinki IT services - looking for a content management system (CMS). At the university, they used Dreamweaver to generate the html pages; I used whatever text editor I had available. After comparing different options, both Helsinki University IT and myself came to the same conclusion to chose Drupal as the content management system for our web sites.Moving to DrupalMoving to Drupal (version 4.6) took me a few weeks, but in the end of 2006, my first Drupal site went online. Starting from that time, adding content to my web site became very easy. I avoided upgrading Drupal and skipped version 6. As I had anticipated, the upgrade to version 7 caused me a major headache (upgrading is supposedly much easier nowadays). Moving to drupal took the University of Helsinki many years, but finally in 2016/2017, the move was/is happening. Barack Obama was much faster: in the autumn of 2009, hardly half a year after he had become president, the switch of whitehouse.gov from a proprietary solution to Drupal was complete.*Is Drupal 7 old?*Here at our university, dead lines must have been moved multiple times and similar to the Western Metro Extension to Espoo , the move likely became much more expensive than planned. The university is using at the moment Drupal version 7, which was relased more than 6 years ago in January 2011. While Drupal 8 is already out since November 2015, the good new is that Drupal 7 remains officially the Long Term Support (LTS) version and thus will receive security updates for many years to come (I would guess for at least five years or so). About 85% of all Drupal sites are still running Drupal 7 and apparently, this number has not shown any signs of decline yet .The move is not complete yetI moved my lab’s web pages in the beginning of this year when the possibility was made available. However, our B3P core facility still runs on “handwritten” html code as we have not gotten permission to move these sites to Drupal (IT is waiting for the HiLIFE research infrastructure funding decisions).Meanwhile, 2.3% of all web sites worldwide use Drupal.*Problems?*However, the system is not free of bugs. Owing to security concerns (PHP security is considered to be porous like a sponge), most of the flexibility that Drupal offers is not available to the content providers: e.g. full HTML or PHP code within node bodies is disabled, which makes the implementation of dynamic content challenging. Luckily, the system has an achilles heel and that is its use of RSS feeds.RSS fees to the rescueRSS feeds with user-provided URLs can be integrated into most pages and surprisingly they allow unfiltered display of html content (including images and css styles). This is the way how I implemented our dynamically updated list of enzymes ( https://www.helsinki.fi/en/researchgroups/lymphangiogenesis-research-and-antibody-development/services-and-resources ) and our list of publications (which displays separate feeds from zotero.org , e.g. a list of featured publications or a list of review articles . Unfortuantely, the feed module doesn’t accept standard atom feeds, but only “old-fashioned” RSS feeeds, which required me to pipe the Atom feed from Zotero through a python script before it can be fetched by the site visitor’s browser.Varnish CacheThe other problem is that the site loads fairly slow. If visitors look for content the site must load with 3 seconds or the visitor is lost. Hopefully the site will scale well since many research groups have not made the switch yet. And it loads slowly despite it using a Varnish Cache . Unfortuantely, the Varnish Cache delays updates from becoming public sometimes for many hours (sometimes even over night). In the 21st century, that is not acceptable. I have set the maximal cache life time to 1 hours for my private Drupal site. The 3 second loading time is likely the best compromise they could find…

Barriers to Electronic Lab Notebook adoption

Thu, 08 Jun 2017 00:00:00 +0000

Our lab has been interested in electronic lanb notebooks (ELNs) for a while. A recent publication in the Journal of Cheminformatics has focused on the barriers to ELN adoption. Especially in the academic world, more than 90% of scientists are still using the traditional paper lab notebook. Biggest barrier to adoption was the cost in terms of money and learning of new habits. Close runner-ups on places 3 and 4 were the implementation effort and security concerns. While the authors are clearly biased (they are developing the open source ELN ELN SciNote ), the barriers to adoption are the same that I experience in my lab and at the University of Helsinki.I was stunned when about 2 months ago I received an e-mail with the news that the University of Helsinki had negotiated a framework agreement with the LabVantage LIMS/ELN vendor Software Point. While I think a university-wide ELN solution is necessary, this deal seems anything but optimal for most research-oriented laboratories at the University of Helsinki. Several labs at the university are using ELNs already for a while and none of them have been aware of the efforts to provide a university-wide agreement for a LIMS/ELN solution. And none of those that already use a LIMS/ELN have been choosing LabVantage, but other solutions ( Labguru , SciNote , eLabFTW ). It would have been helpful to have somebody in the evaluation team, who has actual experience with LIMS/ELNs use (or somebody who has participated in LIMS/ELN development), especially since such expertise exists at the University of Helsinki.Only a few people have been involved in the negotiations while the majority of the stakeholders were not even asked for their input. When I asked explicitly about this secluded operation, the answer was: Very few units (mainly the chronology unit and a person from dept of chemistry) were involved with the purchase at the time even though the information was spread around the university and anyone was welcome to participate and state their needs. However, even though I try to actively follow the IT infrastructure developments, I did not see any announcements anywhere and also searching retrospectively, I could not find anything that would have alerted me and allowed me to participate. The labs contributing most to the international success of Helsinki University are the main stakeholders, but they were ignored. Maybe a little bit more active search for the stakeholdres would have been appropriate.The base package that was negotiated with LabVantage seems to be geared towards routine and clinical lab work, but not towards innovative research. Among the two modules that are mostly necessary for life science research work are the ELN and the storage management. Unfortunately, many life-science specific routines (searching for DNA and protein sequences with blast-like search algorithms) are totally absent from the offer, but are very much needed for life science. The lack of a free API (like eLAbFTW features or SciNote soon will feature) prevents users from incorporating their own, existing code or their own database systems. Every small change would require to involve the LabVantage developers and that will be a very slow and costly process. In reality, this means that shortcomings of the system will never be addressed. The base package can be taken into use by any lab at the university after a single payment of 200€ for each user (no floating licenses, only dedicated users). For our lab that would amount to 2000€, but a low price tag is not a selling point in itself.Within the framework agreement, any lab can pay for the additional modules on its own, but the heft price tag of 17500€ make it unlikely that anybody will do so. I am unwilling to lobby for a joint purchase, because there is no way of knowing, whether these modules would be suitable for everyday lab work. Unlike most other vendors, LabVantage doesn’t offer a free trial of the system. It makes me suspicious, if a vendor doesn’t offer a trial. If the product is good, a trial will convince potential customers to buy. If the product is good, what could be the downside of a trial for the vendor? We have ourselves tested several ELN solutions over the last two years and some systems received very bad feedback by those people who use them every day (e.g. cumbersome data import, unintuitive interface, slow server responses). As a matter of fact, for oligonucleotide management and protein/enzyme storage, we still use the absolutely outdated open source LIMS that I co-authored about 15 years ago as a PhD student ( http://phplabdb.sourceforge.net , now at https://github.com/mbekaert/phplabdb) . In my lab, we use eLabFTW . We have a local installation on the Helsinki University intranet (which can be accessed via VPN from everywhere) and anybody from Helsinki University can get an account there. If you are interested in trying it out, please contact me!The key question remains unanswered: Why were the majority of stakeholders not pulled into the decision-making process?

Forever Young

Sun, 30 Apr 2017 00:00:00 +0000

I was asked by the Novo Nordisk Foundation (specifically by Dr. John Peter Wittschieben) to say a few words from the successful applicants’ perspective during the “ How to Get Funding from International Foundations ” info event, which took place on April 26th in Biomedicum Helsinki.Useful informationTo be clear: The event was very useful. Specifically it was useful due to the detailed information provided by the Novo Nordisk Foundation and JDRF , who presented during the event. In the very beginning, I was surprised to hear our Dean talk in his introduction about the “lucky ones that received the funding”. In my naïveté, I always assumed that funding was distributed according to excellence and ability, not according to luck. While more experienced researchers like Mikael Knipp were able to give good advice, I could not. Obviously, I cannot boast with my own funding rates (which are about 5%, one of 20 applications being successful).**No time for science, too much time for grant proposal writing?**Some participants expressed surprise about the current widespread complaints of researchers about low funding rates, arguing that a rejected application leads to an improved renewed application in the next round. I agree, that the improvement might be substantial for the first few rounds, but then it becomes a game of diminishing returns. I write an average of 20 grant applications in order to get one accepted, and for 15 of these, I rather agree with E.P. Diamandis, who in Clinical Chemistry complained about the $20+ billion loss due to unsuccessful application writing.**Who is a “Young Investigator?”*The other question that - interestingly - was discussed (and which I had wondered about already for years), was the term of “young investigator”. The bottom line was, that everybody is a young investigator who does not hold a full professorship. This might be the only sensible definition, as the average age of principal investigators has been steadily rising during the last decades (see e.g. here ). Many investigators will therefore stay forever young (or at least until they retire).It is difficult to be creative if you are struggling with fundingAlthough I could not convince many (maybe nobody), I objected to the notion that is is desirable to combine the goal of creativity and applicability in academic research. True creativity originates mostly from a primary motivation and utilitarian aspects actually get in the way of creativity. This is not to say, that creative research cannot be very useful. To make them an important criteria in the distribution of funds is just asking too much from the money source, namely to be able to predict the future. Creativity and the push towards “applicability/impact” of research are not only orthogonal to each other, but are pushing into opposite directions. If the research is struggling with funding, it is difficult to be creative. The basic needs for survival need to be met before people can realize their possibilities. In addition, when foundation ask for short term applicability, they appear to me like politicians, who think in terms of the 4 or 5-year election cycle. For much of academic research, we cannot predict its future uses. In addition, potential applications are mostly MUCH more than 5 years into the future. If the push towards applicability results in shifting the balance from basic towards applied science, the pipeline (basic research > applied research > engineering) will dry out from its source. Maybe this push towards applicability will also accelerate the blurring of the lines between the traditional universities and the universities of applied sciences. *I have to side with Marx this time: Nicht das Bewußtsein bestimmt das Leben, sondern das Leben bestimmt das Bewußtsein.

Overrun by the Big Wheel?

Fri, 24 Mar 2017 00:00:00 +0000

Despite focus on internationalization English information about education reform incomplete and lateThe Big Wheel reform is rolling over me and I don’t notice it. There has been some information in English about the process on the University’s intranet . However, during the drafting, most of the documents were initially only available in Finnish and due to the delay caused by translation, foreign staff without English language proficiency was largely excluded from the process. Loosing this input was certainly not helpful, since several goals of the Big Wheel reform are related to internationalization, e.g. harmonizing the degree structures within Europe (“3+2+3 system”) and making the degree programmes internationally attractive and competitive.Excellent students potentially excluded from studying at our UniversityConcluding from the application numbers for the Master’s programmes that’ll start in September 2017, there is still much work to be done to make the programmes “internationally attractive and competitive”. Virtually all programmes reported a decline in applications from Non-EU/EEA countries, which probably will result in much less income from tuition fees than the university would like (Master’s thesis tuition fees at the University of Helsinki are between 13000 and 18000€/year depending on the programme). We probably loose potentially excellent students and there is a diffuse suspicion that the general level of education might suffer. 30 scholarships of varying amounts are available for Non-EU/EEA students. However, only about 10 of the recipients will be able to completely recoup the tuition fee with their scholarship (see here: https://www.helsinki.fi/en/studying/how-to-apply/scholarship-programme) . I also think that the advertisement for the study programmes could be definitely improved.Information about available scholarships: clear enough or confusing? I also fear that many potential applicants were confused about the scholarship programme (so was I, and still am). Our own Master’s programme’s web pages ( https://www.helsinki.fi/en/programmes/master/translational-medicine-transmed ) do not mention the scholarships prominently (or was that on purpose?). Even worse, the link on the Helsinki University’s pages to check whether or not a student is required to pay the tuition fee has been half dead for a while (“You can check this FAQ at the Studyinfo website whether or not you are required to pay tuition fees” (original on this page ). Hopefully it died only after the application deadline finished…Educational reform of the PhD degreeThe Big Wheel reform concerns all three degrees: Bachelor’s, Master’s and Doctorate (PhD). Internationalization is especially relevant to the PhD degree and those Master’s programmes that are entirely in English (e.g. Translational Medicine or Life Science Informatics). Even though about half all PhD students in my unit (Research Programs Unit) are foreigners, hardly any of them knows what the “Big Wheel” is about. Big Wheel discussion at Meilahti campusAfter almost all is set and done, an info event about the Big Wheel was announced for the Meilahti campus (31.3.2017). The e-mail message was exclusively in Finnish. I often have given feedback when important events were not announced in English (more often than not getting no response). That’s why I wrote a message straight to the rector and the vice rector of the university. The e-mail conversation is attached below. Suffice to say that the university is still dedicated to increase internationalization despite this not being without problems…What was discussed at the hearingThe part of the discussion that happened in English was circling around the PhD education. A very valid request was not to fix something that is not broken. In the international comparison, PhD education is for the most part excellent in Finland and the only perceived problem is its length.At the moment a Finnish PhD thesis in life science requires the graduate student to publish in scientific journals. As a consequence, most of the research in Finland is done by PhD students. The exact number and quality of publications required differs between faculties as there is no formal consensus. Typical are 3-5 papers, sharing of authorship is accepted to a certain degree. Not all publications need to be first-author contributions.Finish PhD graduates are competitiveWhile a PhD from a Finnish University is internationally very competitive, PhD graduates are typically much older than those from most other countries. This begs the question: so what? The typical length of PhD studies in Finland has been generally assumed to be around 7 years. However, nobody knows exactly (not even the university itself, since tight rules to register PhD studies have not existed until recently), but there seems to be a very slow movement towards a shorter duration (and less requirements). Strong forces act against shortening of PhD studiesThe fact that the PhD studies last so long in Finland is the result of natural selection. Pushing with regulation for faster PhD education will have many unintended consequences. There are strong forces acting against shortening the PhD studies, especially for highly talented students that aim at an academic career: E.g. the relative ease to get scholarship funding during the PhD studies and the high unemployment among fresh PhDs in Finland.Age limits for PhD degrees for fundingPointed out by Kalle Saksela, a major obstacle to shorting the PhD education is the general funding situation of academic research. With every funding cycle, funding rates are pushing new all time lows. Successful applicants have a very compelling portfolio of high quality publications, which needs time to acquire. However, major competitive research funding (Academy of Finland, ERC) puts limits on applicants (e.g. “no more than 7 years after PhD completion”), which have no relationship to the quality of the application.Four yearsThe very clear message from vice rector Hämäläinen (Jukka Kola had already left the discussion, when it switched from Finnish to English) was that the PhD studies must be shortened in order to reach comparability with other countries. The target is 3+2+4 (3 years for the Bachelor’s studies, 2 more years for the Master’s studies, and then 4 years for the PhD studies). The idea put forward by the vice rector was to simply move some of the studies that are done at the moment under the PhD umbrella into the early postdoctoral period. A big question is obviously who is going to pay for this move? There needs to be a substantial increase in research funding to be able to pay salaries for postdocs unless we want to lower the overall domestic research output. Already now it borders to financial suicide to employ a postdoc with an Academy Research Fellow budget.

Purification and Characterization of Recombinant Proteins

Mon, 20 Mar 2017 00:00:00 +0000

We are organizing (again) a practical hands-on protein purification course from December 4th to 20th. We maximally can accommodate 16 participants, which will form groups of 2 to 4 participants. Each group needs 3 full days to go thru the practical exercises, but day 3 of the course will be overlapping with day 1 of the next group. Venue is Biomedicum Helsinki, rooms A516a1 (where the machinery is) and B318a/b (our lab). We will purify a protein (VEGF receptor 3) using a two-step protocol (affinity chromatography + gel filtration) on the the Äkta Avant FPLC device. On the third course day we’ll assay its interaction with its ligand (VEGF-C) on the ITC (isothermal calorimetry) device. We have given a similar course in 2015 ( http://www.helisci.fi/hbgs/FPLC2015/) . This new course ( https://courses.helsinki.fi/en/DPBM-135/120171139 ) will have a similar structure, but we expand it by one day to analyze protein interactions making use of the new isothermal calorimetry device of our B3P core facility. The documentation and results will be also available from here . Since we can run maximally two samples at a time (we have “only” two FPLC machines), we will have to split the participants into groups (of 2-4 students/group) and repeat the 3-day course several times depending on the number of participants.

No interest (in retrospection and introspection)?

Fri, 17 Feb 2017 00:00:00 +0000

There was much talk about last years “changes” at the university. Surprisingly, nobody seems to be interested anymore in the topic. At least this is the impression that I first got, when I went to the public hearing event at the Meilahti campus. The lecture hall 1 of Haartman Institute, where the hearing was supposed to take place, was completely empty when I arrived. Because only a handful of people had bothered to show up, the hearing had been moved to a table in the nearby Cafeteria. Hardly noticed by anyone, a review group has started its work to analyze the “changes” at the University of Helsinki, which took place during the last one and a half years. I guess the idea was to figure out what preventable mistakes have been done. According to this university source , Jukka Kola, who is the public face for many of the controversial decisions during this period, got to decide himself about the members of the review group. Because of this, the review group will have to be very careful not to appear biased in their report.

1000 times too slow

Thu, 01 Dec 2016 00:00:00 +0000

Helsinki University has outsourced parts of its IT infrastructure to Microsoft. Even if outsourcing is cheaper in the short term than generating equivalent services locally, the net effect is likely negative due to the lost jobs, know how and independence. It doesn’t need a conspiracy to explain this self-destructive behavior, just bad decision criteria, which do not include long term and externalized costs.In its push to upgrade to newer Windows versions, Microsoft ended extended support for Windows XP on April 8, 2014 and the university obeyed by denying network access to XP machines. The argument was that XP was becoming a security risk. At the same time, Windows XP accounted still for about 20% of all Windows installations on this planet ( https://www.statista.com/statistics/218089/global-market-share-of-windows-7/ ). Even in October 2015, well above 100 Million computers did still run Windows XP ( https://en.wikipedia.org/wiki/Usage_share_of_operating_systems and https://www.statista.com/statistics/218089/global-market-share-of-windows-7/ ) without any catastrophic consequences.The ban of Windows XP was a problem, since four of our devices, that we need for research, are still running Windows XP. And there is no way to upgrade the OS without upgrading the equipment (which would cost thousands or tens of thousands of Euros and therefore is mostly impossible in the present tight financial situation of the university). And of course, the software that is needed to operate the devices is not compatible with Windows 7. As a consequence, we can neither remotely operate this machinery nor do automated backups. Even taking the data for analysis to another computer requires the Adidas network .I had contacted IT support well before the extended support of Windows XP ended and asked them to find a solution. Apparently there were different possible solutions and IT support did start to implement them, but because of personnel fluctuations, the project had to be “restarted” several times and different support professionals had different opinions on how to solve this problem. With the big “fire and hire” action at the university, the whole project disintegrated again. This autumn I again discussed our needs with the IT staff, but did not receive any concrete help so far.This Tuesday, I finally wanted to know how difficult it really is to connect a Windows XP machine to the network in a way that would not compromise security, but enable file distribution, backup and remote control. I went to the Institute’s garbage place where broken electronic equipment is gathered and took three old 10/100 NICs and a few ethernet cables. One card and one cable were still functioning and I dropped the NIC into a Ubuntu 16.04 computer and connected it via ethernet cable to one of the XP machines.After manually assigning an IP to the NIC and installing samba onto the Ubuntu machine, I was able to mount the samba share as a drive on the Windows XP machine. Then I just made the samba share available via a web page. All this took about one hour. Not being an IT professional, I spend maybe an additional three hours researching how to do it (samba setup, apache setup, configuration of a secondary NIC, which is not automatic on Ubuntu). This setup fulfills all of our requirements, didn’t cost anything and was implemented within one day.A write-up of the technical details will follow once I get around documenting what I did. Agility is perhaps what is mostly missing when I look at many of our university’s IT projects. Notably I think of switching to Drupal as content management system for the university’s web pages. Sadly, our faculty is still using Dreamweaver to create its web presence and as a consequence many web pages are never updated.

Key project funding

Fri, 07 Oct 2016 00:00:00 +0000

This post is inspired by our recent success in the Key Project Funding call of the Academy of Finland . One of the main time killers for scientists is to apply for money to finance their research. Scientists spend more and more time preparing grant applications because of the growing competition for the shrinking resources.After deducting the time for teaching and administration, they maybe able to spend a few hours each week doing research. Last week over lunch, a friend of mine ask me what our funding rates were. I did not know, because I have been avoiding the inconvenient truth. I calculated today and the depressing result is that they are in the low single digit range and this seems to be a quite average figure (for us, 2015 was an exceptionally successful year and the 2016 number might perhaps still improve since several decisions have not been made yet).Improving academical productivity by increasing the 1600 hours of yearly working time on paper is meaningless if 400 hours of this time are spent in vain, i.e. for unsuccessful grant applications. The financial damage and opportunity costs to the system are enormous and a colleague of my recently pointed me to this 2015 article in Clinical Chemistry , where the monetary value wasted by grant application writing was conservatively estimated for the US to be at least $20 billion per year.Our budget includes new positions for researchers, but we don’t know yet where and when these people will be able to start their work. In theory, the hosting organization (i.e. the Research Program of the University of Helsinki) guarantees the infrastructure. However, the Research Program cannot generate lab space from nothing. The university is just trying to save money by minimizing the floor space it rents. While some people celebrate successful grant applications, my view is more down-to earth: After the grant decision is before the grant decision*.*Citation modified after Sepp Herberger , coach of 1954 soccer world cup winner Germany, who famously stated “After the game is before the game.”

Cloning club - workshop material

Tue, 30 Aug 2016 00:00:00 +0000

Collection of the course materials for the DPBM -organized Cloning Club . There are files in (at least) two different formats for each lecture: PDF and ODP (Open Document Presentation). The ODP file is editable using LibreOffice software. If you want to open it with Microsoft Office, you need to convert it first using either LibreOffice or some online conversion tool (like cloudconvert ). The material by the course organizer (in Open Document and PDF format) is available under the creative commons license (excluding adapted material, which is explicitly marked). Material from course participants (in PowerPoint format) is provided at the terms of the creators. I might add improved versions the meeting/lecture slides later based on participants feedback.

University rankings (and how to manipulate them)

Mon, 29 Aug 2016 00:00:00 +0000

Whow. Helsinki University was again able to improve its position in the Shanghai Ranking and is now number 56. However, even the University’s own press release had kind of a gloomy tune as if this was the last blossom before the final decay. It is true that the basis of the current success has patiently been built by the researchers over the last decades. Nevertheless, when politicians now draw the conclusion that the cuts of the educational budget are responsible for this success, they are probably right.Perhaps the cuts actually did contribute to the surge in productivity: All the scientists that unexpectedly were suddenly unemployed obviously continued to work furiously on their current projects to get their current manuscripts ready for publication. Papers are the overwhelmingly dominant currency in the academic job market. And these unemployed scientists might publish faster than before since unemployed scientists have no teaching duties…However, more importantly, the Helsinki numbers of the individual Shanghai Ranking indicators for 2015 and 2016 differ significantly only the per capita academic performance (publications/number of academic staff) and the number of highly cited scientists. Since the job cuts at Helsinki Universities have been going on already for a while even before the massive cuts of this spring, it appears reasonable to claim, that the 56th position is partly due to the job cuts, which did influence directly and rapidly the number of academic staff.The Shanghai Ranking emphasizes research, whereas in other rankings, Helsinki has even been dropping. E.g. in the QS World University Rankings , Helsinki dropped from position 67 (2014/15) to 96 (2015/16). Between these two rankings, the QS team made “improvements” to their ranking system and these were almost exclusively responsible for the drop if you look at the data closely. They “normalized” the citation ratio per faculty according to the subject, and life science got badly punished by being a “high citation field”. Very simply put, a citation to a paper in Arts and Humanities now counts about 40 times as much as a citation to a paper in Life Science/Medicine. Each of the 5 big fields (Arts & Humanities, Engineering & Technology, Life Sciences & Medicine, Natural Sciences, Social Sciences & Management) contributes now equally with 20% to the final rating in the citation per faculty category (detailed explanation of the normalization from here: http://content.qs.com/qsiu/Faculty_Area_Normalization_-_Technical_Explanation.pdf).Why on earth do they punish a field for having a bigger impact? Papers in the humanities are not cited as much as papers in life science. Maybe this could be due to the fact that their average publication is not as relevant for their own field as is a life science publication for the life science field? I agree that there are cultural differences between fields, but who is to say how much is due to such cultural differences versus low quality or irrelevant research? Exactly that’s what QS World University Ranking’s did by making up “normalization” factors essentially claiming equal relevance.However, all such rankings are easily manipulated. E.g. the citation to faculty (member) ratio can easily improved by outsourcing services that were previously performed by faculty scientists (and that’s what Helsinki University is just doing at the moment). Similar to the impact factor for journals, university rankings are losing their relevance if the goal is to score high and not to excel at research and teaching ( Goodhart’s law : When a measure becomes a target, it ceases to be a good measure).The Shanghai Ranking has been criticized much. It undervalues teaching since teaching performance doesn’t enter directly the calculation at all, and it favours big universities since 50% of the rating are based on sheer numbers which are not normalized to account for the size of the university. Nevertheless it it the only reproducible (and therefore scientific) dataset from the three big rankings ( https://link.springer.com/article/10.1007/s11192-012-0801-y ) since both the QS and the Times Ranking rely heavily on opinion and reputation surveys, which are notoriously difficult to reproduce.What is the take-home message? Helsinki University is probably as good as it used to be during the last decade and the big fluctuations are just artifacts resulting from changed ranking methodologies or resulting from administrative adjustments to the financial realities brought upon us by the Finnish voters in the 2015 parliamentary elections.

Let's beat cancer together!

Sun, 07 Aug 2016 00:00:00 +0000

Sawan and me registered as “The Jeltsch Laboratory” team to the Helsinki Twilight Run , which is a charity event to support the Finnish Cancer Foundation . However, Sawan caught a summer flu and had to skip the whole event. My goal was to stay below 1 hour and I managed. There were actually more participants from the RPU (Research Programs Unit) ; I ran into Tiia and Julia. Maybe we should next year start as a joint RPU team (or whatever the RPU will be called if we really manage to change our name)?

RPU Seminar 2016

Fri, 24 Jun 2016 00:00:00 +0000

Available Downloads

Get the slides in PDF format.

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Cloning Club

Wed, 22 Jun 2016 00:00:00 +0000

Together with the Doctoral Programme in Biomedicine (DPBM) we are organizing in autumn 2016 a workshop and a practical course about cloning (course code 921244).Dates and venue (workshop): Weekly discussion workshop (8 events each 1 to 1.5 hours) starting Tuesday 30.8.2016; venue: meeting room 7 (Biomedicum Helsinki, 5th floor, except 27.09. and the last workshop on 25.10., which take place in BM B136A); 1 creditDates and venue (practical course): Decentralized lab course (at the participants schedule and venue or - for participants without own access to the necessary facilities - in the first two weeks of November in our lab); 1 creditCourse information page: http://www.helisci.fi/hbgs/cloning-club2016 Registration page: https://elomake.helsinki.fi/lomakkeet/71701/lomake.html Detailed course info: PDF Advertisement poster: PDF Course material: Material will be added after every meeting here . Cloning has the appeal of being boring. However, all starts with DNA. Genetic engineering is not only here to stay, but will become more and more important: we are just scratching the surface of its potential. Almost all biomedical research involves DNA constructs: expression vectors to transfect cells, shuttle plasmids to make viruses, constructs to generate transgenic animals.The skill to generate a DNA construct is needed until the arrival of that promised device, which will spit out any plasmid a few hours after you have fed it the plasmid’s sequence. Many new technologies are available and as a result, it is more difficult to choose than in the old days when restriction enzyme cloning was the only option. Today, demands and options are endless and you need to choose the right strategy to maximize success and speed.

Good leadership?

Mon, 02 May 2016 00:00:00 +0000

When I started as a principal investigator at the University of Helsinki , I was advised to take the “Good leadership” course which was arranged by Personnel Training . Together with 14 other research group leaders, I learned between November 2013 and March 2014 from Sanna-Marja Heinimo and other experts i.a. the “skills for effectively developing, coaching, empowering and leading others to getting best results”.At the end of the course, we had a dinner with Jukka Kola , who is now credited for implementating the extensive (and according to many observers overboarding) cost savings that were forced upon the university by the budget cuts mandated by the prevailing political powers.I do not want to discuss here whether such drastic measures were necessary or a less extensive savings strategy would have been sufficient. Even the decision whether to save or to practise deficit spending in an economic downturn is mostly not based on facts but on ideology. In economics, fashion and Zeitgeist are at work in addition to hard data. Therefore, it is not surprising that prominent economists are holding opposing views concerning the effects of deficit spending. But I go off on a tangent here…I simply wanted to express my total disappointment. Not in the savings themselves, but in the way HOW the savings were implemented in relation to the “good leadership” practises that we have been advised to practise.The decisions were not sufficiently openly discussed. Still now, the grounds for many lay-offs remain incomprehensible and controversial (see e.g. this article in the major Finnish daily newspaper Helsingin Sanomat). Since transparency was noticeably absent, the talk about good leadership by the top management of the university seemed to have been hardly more than lip service. I do not doubt that they have the best intentions in mind for the greater good of the university. Just who defines the greater good? Most oligarchs define it themselves, don’t they?So it is not surprising that in the recent workplace well-being survey, the satisfaction with the strategic leadership at the university level (rectors and vice-rectors) was at an all-time low. If the polls would be repeated now, the results would likely be much worse, especially if the fired people would still get a voice. Notably, it is not only the average employee of the University of Helsinki, who does not trust the leadership any more. My feeling is that the distrust now pervades researchers at all career stages. What future is possible with such a constellation?Google is consistently named among the best American companies to work for and they decided to spend millions of dollars and many years to research how to create the best work teams. The single most decisive factor in determining the innovation outcome, creativity and productivity of a team was psychological safety ( see this NYT Magazine article ). Guess how safe university employees are feeling at the moment.When we were talking with Jukka Kola, I was very impressed with his clear commitment towards increased internationalization at the University of Helsinki. However, I already wondered back then how realistic the goal to “actively recruit top international staff” is. Now it seems even more unlikely that this goal can be reached to a meaningful degree since universities start to experience a new wave of brain drain. Even at the students’ level, where the internationalization has made amazing progress in the last 20 years, we might see a decline with the introduction of tuition fees for non-EU/ETA students .

Managing OpenVPN with Network Manger

Thu, 05 Nov 2015 00:00:00 +0000

I just switched back from MacOSX to Ubuntu for work. Mostly for financial reasons. We need more computers at work and a really good PC laptop is just half as expensive as a MacbookPro or iMac. Today I wanted to connect from home to the University’s VPN network and I had a look at the instructions provided by the university.As usually, documentation was virtually absent and what was available was wrong. And exclusively in Finnish ( http://www.helsinki.fi/helpdesk/ohjeet/tietoliikenne_ja_etakaytto/yhteydet_yliopiston_ulkopuolelta/vpn_ubuntu-asennus.html) . From the image (Hardy Heron) it is clear that this page has not been updated for about at least 6 years (Hardy Heron was realased in the beginning of 2008).So what do you do if you downloaded and extracted the hy-vpn-config.tar.gz file from https://ohjelmistojakelu.helsinki.fi?First you need to install a plugin for the Network Manager: sudo apt-get install network-manager-openvpn network-manager-openvon-gnome. Then you go to the Network Manager via the icon in the menu bar on the top right of your Desktop. Below all the available wireless networks, there is an entry “VPN Connections”. Follow “VPN Connections” -> “Configure VPN” -> “Add” -> “Import a saved VPN configuration” -> “Create”. Then select the “openvpn.conf” from the downloaded and extracted files. After that, fill in the rest of the dialog box: User name, Password. For the CA Certificate, select the “HY-vpn-CA.pem” file from the downloaded files (you should have put it first somewhere safe, e.g. to “/etc/openvpn”).One problem that people are complaining about is the fact that the import does not honor the “redirect-gateway def1” directive and as a consequence you won’t be able to connect anywhere (I guess this is due to the Network Manager using dnsmasq and dnsmasq is apparently not smart enough to realize that it should send the queries somewhere else now). That’s why people are complaining that Network Manager doesn’t work to route all traffic via the VPN network. The box that you need to uncheck for this to work is well hidden: It’s in the connection editor dialog under the IPv4 Settings tab -> Routes (at the bottom right) -> “Use this connection only for resources on its network”. Why on earth do they have to call it in a way that nobody understands its meaning? Why not to call it “Do not route all traffic through this VPN connection”? I also had to check the box that said “Ignore automatically obtained routes”, although I don’t know why…As usual, setting up the OpenVPN sucks and the important tunneling back of VPN traffic needed to be added manually on the OpenVPN server:iptables -t nat -A POSTROUTING -s 10.8.0.0/24 -o eth0 -j MASQUERADEI did it by making an additional file called openvpn2 in the /etc/network/if-up.d/ directory with the following content:#!/bin/shiptables -t nat -A POSTROUTING -s 10.8.0.0/24 -o eth0 -j MASQUERADEOf course you can still start and stop the VPN via the command line. However, since systemd, the password entry is not straightforward. When you execute sudo systemctl start openvpn.service you need to execute (e.g. in another terminal) sudo systemd-tty-ask-password-agent and enter your password there. That’s clearly a kludge until they get a decent password agent…

The new Finnish government cuts university funding by around 500 million € (or not?)

Thu, 11 Jun 2015 00:00:00 +0000

UPDATE: It appears that some of the party representatives that were the source of the information in this article have not been reflecting the official positions of their respective parties (in other words: they were talking BS without having any authorization to do so). In reality, the coming cuts and their sizes are going to be determined only during this coming fall season.

2-week Lab Course

Tue, 30 Dec 2014 00:00:00 +0000

I had no idea how much work it is to organize a practical lab course. Had I known, Pirjo would have had a much harder time to convince me to give this course for the Doctoral Programme in Biomedicine (DPBM)l . Kari had warned me… The accompanying lecture course had been running from September to November. The practical course had been offered with 16 free slots, but that was totally unrealistic given that we were confined to my 23.7 square meters of lab space. Teaching lab space is available, but without equipment and all the other infrastructure that is needed for such an undertaking. 8 people registered to the practical course and - luckily - half of those pulled out in the last moment with insufficient possibility to commit to the heavy workload that the course required. Thus we ended up with four students and three projects. Under no circumstances would we have managed with more.The idea was to offer each participant the possibility to realize his own DNA cloning and protein expression project. Something that would be relevant for his own PhD studies. For that matter, I had meetings with the three groups one month in advance to plan the cloning and to order the necessary materials. We were working in parallel on the following three projects:

Practical Molecular Biology and Genetic Engineering

Mon, 08 Sep 2014 00:00:00 +0000

Collection of the presentation slides for the DPBM course Practical Molecular Biology and Genetic Engineering . There are files in (at least) two different formats for each lecture: PDF and ODP (Open Document Presentation). The ODP file is editable using LibreOffice software. If you want to open it with Microsoft Office, you need to convert it first using either LibreOffice or some online conversion tool (like cloudconvert ). All material is available under the creative commons license . I might add improved versions of the lecture slides later based on participants’ feedback. The slide about restriction enzymes (REs) and how to calculate the necessary RE amounts to digest a certain amount of DNA is in the file of Lecture 1.

One firewall to block them all

Tue, 06 Nov 2012 00:00:00 +0000

Helsinki University’s firewall prevents employees from workingWhile I was lying in hospital with a broken calf-bone I couldn’t get any work done because of the Helsinki University’s firewall. Even if the Android OpenVPN client would have allowed me in, I wouldn’t have been able to work. The purpose of a VPN is to allow remote clients the same access to the LAN resources as those machines, that are physically located in the LAN. Obviously Helsinki University doesn’t think so and doesn’t give VPN clients equal privileges. In my case it meant that I cannot ssh into my work computer. This makes remote work expensive, because it required my boss to buy a laptop for me just because the firewall between HY-VPN clients and local machines blocks ssh connections. Without this restriction I could do all the work from my 400€ tablet using e.g. nomachine Player).The work-arounds failed alsoIf I had managed to login into one of the University’s UNIX servers (myntti, kruuna, klaava or ruuvi), I could have logged into my work computer from there. However, my Android ssh client ConnectBot was not able to ssh into them. I presume this to be the fault of my mobile phone network provider Tele Finland , because I couldn’t log into my own ssh servers either (which I normally can, when my Android is connected via WLAN). Once I can connect via ssh to my work computer, I can establish a reverse ssh tunnel and use X Windows or the NoMachine Player to do all the work I usually can when sitting in the laboratory in front of my work computerPlex and no end of video playback troubleHowever, I couldn’t get the OpenVPN configuration right on Android and neither could the helpdesk support to this date. So I was totally bored in the hospital and since we use Plex at home as our media center, I decided to watch some movies. However, Plex is still after four years development in beta and we had our fair share of trouble with media playback. Also this time: I couldn’t play back a single movie or a single song using the Android client . It made the connection to our (Ubuntu 10.04) plexmediaserver without problems, but the only thing that worked was the “Photos” section. By trial and error, I found out that a part of the problem was, that the videos were in Apple’s QuickTime format (they had been encoded on a Mac). So I was looking for a way to batch-convert hundreds of files from .mov into .avi. Certainly this would be faster than filing a bug report and waiting that the Plex guys fix the problem. QuickTime is anyway dead, isn’t it? ffmpeg was certainly the way to go, but Google flooded me with hits concerning batch conversion and the problem was finding the one that works. There is unfortunately lots of crap and noise on the web. The following one-liner did work:find . -name '*.mov' -exec sh -c 'ffmpeg -i "$0" -sameq "${0%%.mov}.avi"' {} \;

½ year and 1000+€ for Win7 & Office 2010

Mon, 02 Apr 2012 00:00:00 +0000

In the beginning of 2011 I bought a netbook ( Lenovo IdeaPad S10-3t ). I bought it with my own money. It was preloaded with Windows 7 Starter Edition. Because I prefer to use Ubuntu , I shrank the Windows 7 partition and installed Ubuntu as my primary OS. I installed the University-licensed Microsoft Office XP, for which there were still installation media around in our research program. There are only two occasions when I boot into Windows: when I needed to work on collaborative publications or grant applications at home with my co-authors using Microsoft Word or when there is a program that has no equivalent on Linux (which has rarely happened during the last years).However, last October, more and more compatibility problems appeared between the aging Office XP and the newer versions of Office, that use the new XML format (.docx). On one occasion, after my boss had opened a Word file (created by Office XP), modified it and send it back to me (using compatibility mode), it became uneditable in Office XP. Word would crash whenever I tried to edit two of the three embedded images. In fact, I spent hours of recreating an editable version of that document from scratch.That was when I decided to upgrade my privately owned computer’s Windows and Office versions. Helsinki University’s license agreement with Microsoft allows staff and students to run Windows and Office on their home PC. To university researchers, it happens all the time that they need to work from home. In fact, I wrote almost a complete research paper ( Jeltsch et al, JBC 2006 ) from home. Thus it should not be difficult and not expensive to upgrade from Windows 7 Starter to Windows 7 Ultimate and from Office XP to Office 2010, right? Helsinki University wants to get higher and higher in the [Alma intranet pages]( http://www.topuniversities.com/university-rankings/world-university-rankings/2011?page=1>international rankings. Therefore, one might think the University would have made sure their researchers have easy access for the right tools to do their job. WRONG!Helsinki University has provided instructions on their Ohjelmistojakelu page of the university. Under the <a href=) (Home Use Program) link hides the “Microsoft Home Use Program and software delivery to members of the staff”. I downloaded the file (“koodi.txt”) which is a text file cotaining a code (something like “XXX0000”). With this code I went to the Microsoft Home use Program site. I had to type in my work e-mail address and the code and I received the following error message: “We are sorry, but we are unable to complete your request. the following problem(s) exist: - Please contact your benefit administrator to learn if you are eligible and to retrieve your program code.“I phoned the helpdesk of the University to ask what is wrong. The answer: “The University and Micorsoft are negotiating a new licensing deal and the old code doesn’t work anymore and the new code is not yet there.” How long will it approximately take for the new working codes codes to appear? “A few weeks.” I waited a few weeks. To be precise: I waited six weeks. I went through the same procedure as before. But the code still did not work. Retrospectively, I suppose that the helpdesk’s first answer was wrong: The codes were probably still fine, but the instructions on the university’s pages were wrong (they sent me to the wrong page to type in the code and at the time of this writing - 5 months later - the university’s pages are still wrong).In the beginning of the new year I submitted a formal support request to the helpdesk. I received the following answer:Hi MichaelUniversity of Helsinki has made a new agreement with Microsoft (moved from MSCA to EES) starting this month and now that our agreement is changing codes won't work. I assume we get new codes to our new agreement from Microsoft after all paper work is done, and this will take approx. couple of weeks or so.All we can do now is wait, you can check in february if Home Use Program -option is working. Sorry for the inconvenience.Best regards,Tommi also send me the Alma link with the instructions . I tried several of the links in the document (which were links to sites where one could order Windows and Office installation media/downloads), but already the first link was broken: Microsoft Windows operating systems: e-Academy (no CD/DVD option, only downloadable versions). It is still broken at the time of this writing.The other option (“Microsoft Home Use Program HUP (Digital River, also installation medias)”) linked only to the instructions that I already knew (and which do not work). Because apparently nobody had ever tried before to leaglly aquire Windows and Office for home use via this program, I went in March together with my computer to our physical help desk at Meilahti campus. Iivari was very friendly, but the only thing he managed to do was to replicate the problem and to convice somebody that there is a problem that should be looked at. A few days later he sent me the link to a page from where I could order Windows and Office for 20€/DVD: https://hup.atea.fi/ .This link I have never found anywhere in the university’s online instructions (as I learned later, it is somewhere there, but almost impossible to find). I am not surprised that otherwise law-abiding citizens of this country use illegal versions of Windows/Office at home if it is so difficult to be legal.I received the DVDs via Post a week later (I had to go to the post office and to pay there the 20€/DVD).Before I installed anything, I made a disk dumpdd if=/dev/sda of=/dev/sdbof my entire hard drive (250 GB hard disk, it took 20 hours via USB). Because I had Windows 7 Starter installed on my computer, I first tried to use the anytime upgrade . For this I actually only would have needed the license key, but not the physical installation disks. When I typed in the key, it started the upgrade, but failed without any details. So I decided to run the upgrade advisor (a program from Microsoft that determines whether your computer is “good” enough for the upgrade). The only thing it found was that I was short on disk space. So I freed another 5 GB by uninstalling software (mostly the bloatware that was put there by Lenovo). The second attempt also failed without any specific error message. I had no way of knowing what was the reason.So I tried a clean custom install. First I needed to transfer the Windows 7 install DVD to a USB stick (my computer has no CD/DVD drive and I or my lab doesn’t own an external CD/DVD drive). Fortunately this is easier with Windows 7 than with Windows XP. However, not all USB sticks seem to be equal and the first USB stick I tired (Verbatim) was rejected by the tool I used. I followed these instructions . Then I booted from the 4GB stick and started the upgrade. Everything went fine until the very end, when I needed to reboot and I was greeted with “Your Windows 7 install is broken. Do you want Windows to fix it?” Then I made a bad decision: I said yes. After fixing, nothing worked anymore. Upon rebooting, there was only a blinking black cursor.OK, if I cannot upgrade, I can do a fresh install. I wiped my hard drive clean and started the install. Everything went fine until I had to type in the product key. It complained that it is not a valid product key. Of course I had not thouroughly read and understood the pages at www.atea.fi . Probably because they are only in Finnish. Apparently, the University’s deal with Microsoft does not provide the staff with full installers, but only with upgrade installers. Consequently I need to keep my old Windows version around for the install. Luckily I had my diskdump. I wrote it back to the hard drive. This took only about 6 hours.This Monday I went (together with my laptop) to the local computing support. Perttu enlightened me about the possible upgrade paths to Windows 7 and tried to do the custom install using an external DVD drive. And it worked! Hallelujah! It took several reboots, but finally I had a running Windows 7 Ultimate. Installing the drivers took also about three hours. It took an eternity to download the drivers from Lenovo’s site, despite them being akamaized. Maybe they didn’t pay their bills. Now I just needed to create an iso image from the Office 2010 DVD, move it over to the computer and start the install, which went flawlessly this time.I presume that the first time I tried the custom install, the system was somehow compromised by the failed anytime-upgrade. Who knows. 500 Million lines of code, that nobody really understands anymore. It’s close to a miracle, that Microsoft is managing to keep Windows afloat.Of course the Windows installer had screwed up my grub boot loader and I had to start the machine from a System rescue CD on a USB stick and write back the MBR from my disk dump:dd if=/dev/sda of=/dev/sdc bs=512 count=1I still don’t exaclty know now, whether the Windows 7 Starter Edition does or doesn’t qualify for an upgrade using the University licensed upgrade plan. I stupidly assumed that if a 10 year old Windows XP Home qualifies, a Windows 7 Starter edition would too.The whole procedure lastet about half a year and taken together, I spent maybe seven to ten days of work for it (about half of this time during working hours, the other half during my weekends). Let’s estimate the real costs including the hours I had to put into this Windows 7 & Office 2010 installation: conservatively at least 1000€. The system is broken and the worst thing is, that there is nobody to blame and nobody who can fix it. Maybe Helsinki University should invest some energy and time into the development and adoption of open source Operating Systems. After all, the most popular one (Linux) was started by somebody from Helsinki University .

Adjunct Professor

Wed, 04 Jan 2012 00:00:00 +0000

Since December 13th, 2011, I am an adjunct professor (Finnish: dosentti ) at the University of Helsinki. This is not a tenured position, but a title, which requires a certain amount of scientific success after completing the PhD and teaching experience ( more about this in Finnish ).

How I became an "Adjunct Professor" ("dosentti") at the University of Helsinki

Wed, 04 Jan 2012 00:00:00 +0000

Compared to getting my PhD degree, the “dosentti” thingy was easy. I started in the beginning of 2011 and received the title the same year in December. I don’t know whether the process differs between different Finnish universities and some of the formalities might be specific to the University of Helsinki , but nevertheless, below I list the steps I took to get the title. There are also instructions available from here .

Academic Portfolio 2011

Tue, 08 Mar 2011 00:00:00 +0000

This is my Academic Portfolio in PDF format. Since it is public, I had to black out confidential information concerning confidential ongoing collaborations, my research plans and the contract research I am doing for Vegenics Ltd./Circadian Technologies . I assembled this for my application for the title of Adjunct Professor .

Äkta Explorer FPLC core facility

Wed, 26 Jan 2011 00:00:00 +0000

Nowadays I spend much of my time at work on the purification of proteins which regulate angiogenesis and lymphangiogenesis . Therefore, I am taking care of the necessary machinery that the Molecular Cancer Biology Research Program owns: the fast protein liquid chromatography (FPLC) machine. Prof. Jorma Keski-Oja acquired about 15 years ago one of the first (and in 2010 discontinued) Äkta Explorer machines from Swedish producer Pharmacia (who merged in 1997 with Amersham to become Amersham Pharmacia Biotech, who was in turn bought by GE Healthcare in 2004). In the year 2000 the equipment moved from the Haartman Institute into the Biomedicum Helsinki . While I have maintained web pages for this piece of research infrastructure for the last five years (including online reservation and data backup), they were only available from inside the Helsinki University network.Now, I managed to have web pages about the Äkta Explorer FPLC core facility added to the web site of the Medical Faculty . At the moment, we are adding the WAVE cell culture system to our facility to be able to produce large amounts of cells/cell culture supernatant (up to 25 liters of bacterial, insect or mammalian cell culture) for protein production.

HBGS course

Mon, 10 May 2010 00:00:00 +0000

All documents related the the HBGS course Tags in protein expression, detection and purification. Most documents are available in both PDF and OpenOffice format. Feel free to repurpose the documents. They are licensed under the Creative Commons Attribution-Noncommercial-Share Alike 1.0 License .

Recombinant proteins

Fri, 25 Sep 2009 00:00:00 +0000

A dynamically updated list of proteins used to be here, but I shut down the communication to our lab’s database server due to security concerns.

The Molecular/Cancer Biology Lab 2008

Sat, 11 Jul 2009 00:00:00 +0000

The Molecular/Cancer Biology Lab 2008

Mon, 11 May 2009 00:00:00 +0000

The Molecular/Cancer Biology Lab 10 years ago

Tue, 05 May 2009 00:00:00 +0000

I cleaned my computer files and I found this historical photo collage…

And here is another historical document. It’s an article about the Alitalo laboratory in the “Yliopisto” magazine from September 2002:

PhD Defence (November 29, 2002): Lectio praecursoria

Mon, 07 Apr 2003 00:00:00 +0000

Michael Jeltsch’s PhD thesis

Mon, 25 Nov 2002 00:00:00 +0000

My doctoral thesis has been published: Michael Jeltsch VEGFR-3 Ligands and Lymphangiogenesis, Helsinki 2002. The public defence will take place in Biomedicum, Helsinki, on November 29th, 2002.

Lab seminar: Cystine knot proteins

Thu, 22 Aug 2002 00:00:00 +0000

Tyrosine Kinase Receptors

Sun, 07 Apr 2002 00:00:00 +0000

Lab seminar: Chicken kick ass

Wed, 13 Jun 2001 00:00:00 +0000

A 10 min presentation of my projects

Tue, 07 Nov 2000 00:00:00 +0000

Available Downloads

Get the presentation in PDF format.

Download PDF

Projects in the Molecular/Cancer Biology Laboratory

Fri, 31 Dec 1999 00:00:00 +0000

Available Downloads

Get the poster in PDF format.

Download PDF

The Alphabet of Angiogenesis

Thu, 31 Dec 1998 00:00:00 +0000

Available Downloads

Get the poster in PDF format.

Download PDF