Video on Michael’s Domain

Exporting from Avidemux to MP4

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

For some reason, Helsinki University’s Unitube crashes when trying to upload an MKV file. The same used to work last year… Only proprietary formats seem to be ok (such as MP4). This creates lots of additional work for me, since I use open source tools to edit my lecture recordings (mostly to cut out unnecessary parts).However, to create an MP4 file, I need to transcode, which is a time-consuming process that requires changing many of the default settings. Below the process using the Open source software Avidemux:

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.

The Staden package on Ubuntu for bioinformatics dinosaurs

Wed, 27 Jul 2016 00:00:00 +0000

Mostly we use the SnapGene software when we check the sequences of our DNA constructs. However, sometimes SnapGene’s alignment view is not flexible enough and then I fall back to using the ancient Staden Package . I just had upgraded from Ubuntu 14.04 to 16.04 and hence did not have Staden installed. I was pleasantly surprised when the installation of Staden took only about 15 seconds because finally - thanks to the Debian Med team - Staden is available from the universe repository (actually already since October 2014).sudo apt install stadenStaden is clearly not as intuitive as it could be, but it is very powerful and lends itself to automated processing of data. If you have the opportunity to learn it, I would encourage you to do so. The Finnish CSC recorded the Staden course from 2004, in which I participated and you can get the recordings from Funet TV . I just had briefly considered switching from Ubuntu to SuSE because of the ongoing wireless connection debacle that Canonical can’t seem to fix, but considering how non-trivial a manual install of Staden is, this is a big plus for Ubuntu. There are obviously dedicated Linux distributions for bioinformatics purposes, but they all tend to lag behind the latest and greatest developments of the major distros.

Chicken embryo

Tue, 18 Aug 2009 00:00:00 +0000

Through a hole in the egg shell you can visually follow the complete chicken development. Click the video link below to see the heart beat!

youtube to iPod and how to check video files

Mon, 23 Feb 2009 00:00:00 +0000

I was trying to extract the audio file from some youtube videos in order to play it back from my iPod shuffle. I tried various methods (including the otherwise quite versatile VLC Player , but finally settled on the following two step procedure:1. Download the flash video (file ending .flv) file to your local disk. You can use any method to accomplish this task, but as usual Firefox has the perfect plug-in for this task: Download helper .2. Extract and convert the audio file with ffmpeg using the following command: ffmpeg -i video-infile.flv audio-outfile.mp3 It is also possible to convert the flv file into a mpeg file. You need to do this e.g. if you want to import the video into iTunes . For some strange reason Quicktime can play Flash Videos, but iTunes doesn’t allow their playback. The command is almost the same: ffmpeg -i video-infile.flv audio-outfile.mpegAnother nifty usage of ffmpeg is to check video files for corruption and other problems:ffmpeg -v 5 -i file.avi -f null - 2>error.log

Cutting mpeg movie files (mpgtx)

Wed, 04 Apr 2007 00:00:00 +0000

I recorded a documentary from TV as mpeg2. To be able to distribute it via the internet I need to shrink its size and I am using the DivX codec. But first I wanted to trim the beginning and the end. I used mpgtx , a very handy command line tool. There are Suse RPMs from Packman . The command was mpgtx -s tutkittu_juttu.mpg [00:22.50-26:55.00] -o cut.mpg

ksubtile, subtitles and subtitle format (srt, mplayer)

Wed, 04 Apr 2007 00:00:00 +0000

There are heaps of subtitle editors for Windows, but I found only one usable for Linux: ksubtile. It’s not perfect but usable. It uses SubRip format (*.SRT). In these files subtitles have a running number, end- and startime down to milliseconds given for each subtitle.

Mplayer is probably the best video player (and mencoder the best encoder)

Wed, 04 Apr 2007 00:00:00 +0000

Because the videodata recorded by dunerec is in some strange mpeg flavour it occupied quite a bit of diskspace. 2 hours approximately 5 GB. that is why I was looking for an easy way to convert the mpeg into divx. After unsuccessfully palying with transcode, I managed with mencoder. Mencoder is included with Mplayer and there is an RPM for Suse Linux 9.1.

Self-playing DivX movies on CD (movix, autostart, vlc)

Wed, 04 Apr 2007 00:00:00 +0000

I needed to put a DivX movie to a CD, that would play on virtually all computers without the need to install the DivX codec or a movie player. There is software available to make this kind of CDs with nice GUIs, etc. but the software I tested is far from user-friendly. The two easiest methods are:

Watching, ripping and converting DVDs (xine, mplayer, mencoder, dvd, iso image)

Sun, 12 Nov 2006 00:00:00 +0000

Both xine and MPlayer can play DVDs directly, but xine has a DVD navigation. In Mplayer you need to specify which movie (VOB file) you want to play:xine dvd:// mplayer dvd://3 If you just want to temporarily store the DVD on your hard disk it might be sufficient to create a DVD image:dd if=/dev/dvd of=rosenstrasse.iso The image can be mounted as follows:sudo mount -o loop rosenstrasse.iso /media/temp/ Xine can play a DVD from an iso image directly (without mouting the image):xine dvd://media/isos/movie.iso Note that you need to specify always the complete path even if the movie is in the current directory! Mplayer can play the individual VOB files from the image (however without subtitle support). I couldn’t make Mplayer to accept the iso image as dvd.For conversion to e.g. DivX/XviD the easiest is to use Mplayer/mencoder. First I extracted audio:mencoder dvd://1 -ovc frameno -o frameno.avi -oac mp3lame -lameopts abr:br=128 Then the 1. pass encoding:mencoder dvd://1 -nosound -oac copy -o /dev/null -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=800:vhq:vpass=1:vqmin=1:vqmax=31 -vop scale -zoom -xy 640 -vf pp lb Then the 2. pass encoding:mencoder dvd://1 -oac copy -o file.avi -ovc lavc -lavcopts vcodec=mpeg4:vbitrate=800:vhq:vpass=2:vqmin=1:vqmax=31 -vop scale -zoom -xy 640 -vf pp lbIt is more difficult to extract the subtitles. You can either extract them as images (easier but bigger filesize) or then convert these images into textfiles (requires an OCR step).Extract subtitle images (from mounted iso image in this case):cat /media/temp/VIDEO_TS/VTS_01_?.VOB | tcextract -x ps1 -t vob -a 0x20 > movie.ps1 Convert subtitle images:subtitle2vobsub -i /media/temp/VIDEO_TS/VTS_01_0.IFO -p movie.ps1 -o movie_name Copy metadata:cp /media/temp/VIDEO_TS/VTS_01_0.IFO movie_name.ifo Play from VOB file directly:mplayer /media/temp/VIDEO_TS/VTS_01_1.VOB -vobsub movie_name -vobsubid 0 Play from avi file:mplayer movie.avi -vobsub movie_name -vobsubid 0