journal club
Posted by razor | Filed under Bioinformatika, English
Yesterday we had another journal club, and I gave a talk [again]. Now on next generation sequencing and large scale genome projects. Basically I just threw a bunch of links, ideas and names at the audience. This was the 10. journal club and we had 10!!! participants. Somehow the word pathetic came into my mind during the presentation, as usual. I also uploaded an older presentation. Enjoy!
Tags: conservation, dna, expression, genome, journal club, nextgen, presentation, sequencing, topology
open science: doop
Posted by razor | Filed under Bioinformatika, English
The Database of Orthologous Promoters needs some debugging, cleanup, new features and updated data. I decided that I will publish all notes, problems, developments, data, graphs and results here, as an Open Science experiment. First, the main lines of future development are the following, in no particular order.
- The web search interface needs some debugging, as some of the features which used to work in the oooold version [or before the server crash] are not working now. Particularly the GeneOntology analysis in one very special case, and the BLAT server, used for the promoter sequence search.
- Maybe we should integrate the DoOP and DoOPSearch services. Basically it’s just a pain in the ass to use two separate domains. A simple redirect, and that’s all, problem solved.
- The underlying MySQL database needs some refactoring. I suspect it’s not the optimal version what we have now, and it won’t be easy to extend it and add new features, like known transcription factor binding sites, alternative promoters, or multiple reference species for the plant section.
- The Bio::DOOP API also needs some debugging and cleanup, maybe some more features. EMBOSS version checking, more flexible queries, some integration with BioPerl, and maybe the TFBS module [not sure about this]. Adding documentation.
- Adding much, much more documentation, describing the database, motifs, promoter analysis methods, etc.
- Adding a simple query-hit alignment view for the motifs, found during a search.
- Making it work as a web-service, registering it in Biocatalogue, making it usable for Taverna/myExperiment, and also for Galaxy. Possibly a DAS server. Now I’m a little unsure about these, need to read some stuff, like the Semantic Web by O’Reilly and a bunch of tutorials.
- Developing a more complex plant section, with more reference species [rice, grape, poplar, etc] as plants are not nearly as nice as chordates, concerning their genome evolution, polyploidy, orthologous groups, etc.
- Integrating data from other dabases, particularly JASPAR, PLACE, PAZAR, PlantCARE, ORegAnno, ABS, AGRIS. That’s a lot! Some clustering and cleaning of these data is also needed.
- And last, but not least, the database needs some more up-to-date data both in the plant and chordate section.
Nice list, I think I’ll go with the MySQL redesign first, and try to create some normalized tables and stuff.
Update: I also started to upload the various DoOP related codes and scripts to github. See here.
Tags: database, doop, open science, promóter, redesign
atemporality
Posted by razor | Filed under English, Filozofálás
Keynote of Bruce Sterling on atemporality at the Transmediale 2010 festival. [Sorry for the fucking autostart.]
Tags: atemporality, bruce sterling, transmediale, video
stéphane gladyszewski
Posted by razor | Filed under English, Művészkedés
The work of Stéphane Gladyszewski, a multi-disciplinary artist from Montréal, can be seen at Trafó, Budapest, during the festival Temps d’Images. He mixes sculpture, photography, contemporary dance with digital installations, multimedia and video into an illusionary, dreamlike performance. The titles of the short performances are In Side and Aura. You can find more information on the site of Trafó, and a more detailed analysis of the performances is available here. I already have the tickets.
Tags: art, Budapest, contemporary, dance, multimedia, performance, stéphane gladyszewski, Trafó
diy bioinf pt 3
Posted by razor | Filed under Bioinformatika
[A while ago I started a series of posts about the basics of bioinformatics, basic tools, programming, etc. It is intended mainly for my hungarian readers, with only limited knowledge in bioinformatics, so the posts are in hungarian.]
Eljutottam odáig, hogy kirakjak még egy kis bioinformatikai alapozást ide, az első két rész itt és itt található. Írtam a BioPerl és a shellscriptek hasznáról is, most néhány egyszerű scriptet ki is rakok a következő napokban amik [nálam legalábbis] sűrűn előforduló, de nem túl komoly feladatokra jelentenek megoldást.
Az első script egy fasta fájlból kiszedi egy tetszőleges azonosítókat, kulcsszavakat tartalmazó lista alapján a megfelelő szekvenciákat, majd azokat kírja egy másik fájlba. A ‘-i’ kapcsoló a bementi fájl, a ‘-o’ a kimenet és a ‘-l’ a lista, ami az azonosítókat tartalmazza.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 | #!/usr/bin/perl use Getopt::Std; use Bio::SeqIO; getopts('i:o:l:'); my $in = $opt_i; my $out = $opt_o; my $fasta = Bio::SeqIO->new('-file' => "$in", '-format' => 'fasta'); my $output = Bio::SeqIO->new('-file' => ">>$out", '-format' => 'fasta'); my $list = $opt_l; my @list = (); open LIST, $list or die "$0 : can't open file $list : $!\n"; while (<LIST>) { chomp; my @line = split; push @list, $line[0]; } close LIST; @search_patterns = map { qr/$_/i } @list; while (my $seq = $fasta->next_seq()) { my $id = $seq->id(); for my $searchobj (@search_patterns) { if ($id =~ /$searchobj/) { $output->write_seq($seq); } } } |
A script nagyon egyszerű, a lista tartalmát beolvassa egy tömbbe, majd a map segítségével egy reguláris kifejezés listát kreál belőle, utána pedig a BioPerl segítségével megnyitott fasta fájlokat egyesével végigrágva kiszedi azok azonosítóját és megnézi, hogy szerepel-e benne a lista valamelyik tagja. Ha igen, akkor az adott szekvenciát kiírja a kimeneti fájlba.
Tags: Bioinformatika, bioperl, diybio, perl, script
information underload
Posted by razor | Filed under Agymenés, English
OK, with Google Buzz here, I have to do some drastic cleanup in my various networks, pages, feeds, contacts, etc. So here are the rules, nothing personal, if I remove you, it doesn’t [always] mean I hate you. This will take some time, but everybody will be happier at the end.
- My wiw profile will be deleted. Simple as that.
- I won’t push my Google Reader shares, last.fm likes, etc to twitter.
- Twitter is for SCIENCE and CYBERPUNK, so I’ll remove blog accounts, “friends” I’ve never met IRL, people only posting once a month, etc.
- Friendfeed is also for SCIENCE, so I’ll just remove everybody not connected to bioinformatics, genomics, biology.
- I’ll happily add anybody on Facebook, and just ignore it, and ban all the shitty applications, as it is too much a pain in the ass to completely delete the profile.
- del.icio.us and last.fm stays, deviantart goes away.
- I’ll clean up my gmail contact list, and will allow only people explicitely approved to chat with me [mainly family and friends (yes, IRL friends)].
- I’ll remove RSS feeds with more than 2 posts a day (they tend to be just reblogs, short quotes, pics, videos anyway), feeds without content for at least 2 months, and will not follow any share.
- I’ll also delete some more profiles on various sites, if I can.
Sounds like an addict making his next resolution, doesn’t it?
Update: turned off Buzz too, and Twitter is also for altporn and fetish models and industrial music, of course, that’s almost cyberpunk.
Tags: buzz, google, information underload, socialnetwork
link and video dump
Posted by razor | Filed under English, Linkdump
Cleaning out various link collections, notes, txt files, bookmarks, etc.
- Open Researcher Contributor Identification Initiative: an open and independent community effort to standardize researcher identification.
- DIY Bio: A Growing Movement Takes on Aging: H+ Magazine reports on the DIYbio movement.
- Outlaw Biology at UCLA Symposium: DIYbio blog on the Outlaw Biology symposium at UCLA.
- Craig Venter at TEDMED 2009 on synthetic life.
- Synthetic biology will bring us a slimy, moist future: Wired UK on synthetic and DIY biology.
- Genetics projects of Ben Fry, who works on data visualization, graphic design, statistics, computer science, Processing, etc.
- Nonobject Design Fiction Book: The principal objective of the book is to stimulate thought: What is an object? Why do we desire what we desire? Why has “functionality” been defined in such a historically narrow way? What is beauty?
Tags: dataviz, design, diybio, genetics, orcid, synthbio, tedmed
oa magyarország
Posted by razor | Filed under Filozofálás
Turkáltam a zinterneten és hirtelen beütöttem a keresőbe az “open access” és Hungary/Magyarország szavakat, aminek a következő lett az eredménye.
Van egy Digital Repository Infrastructure Vision for European Research (DRIVER) nevű piszmogás, amit a hetes EU keretprogram támogat(ott), és van egy Magyarországról szóló rész is, ahol igen sok a “Start text here” szöveg, de azért némi információt is tartalmaz. Itt van például az open-access.hu oldal vagy a HUNOR (HUNgarian Open Repositories) program, ami a magyarországi nyílt hozzáférés kialakítására lett kialakítva. A DOAJ alapján pedig 12 darab magyar kiadású OA folyóirattal rendelkezünk.
További turkálás után rábukkantam a Könyvtár, Információ, Társadalom nevű hírlevélre, ami egészen naprakész és sok érdekeset ír a nyílt hozzáféréssel, folyóiratpublikálással kapcsolatos dolgokról is.
Ezek ellenére kissé az az érzésem, hogy felénk nem nagyon foglalkoznak a problémakörrel, rendszeresen a klasszikus nyavajgásokat kapom, ha megemlítem a dolgot (drága, hová lesz a minőség, ellopják, stb).
Aztán egy pillanatig azon fantáziáltam, hogy mi lenne ha az MTA bevezetne valami ilyen szabályozást, esetleg az általa kiadott folyóiratokat a PLoS-hoz hasonlóan TOPAZ platformon publikálná nyílt hozzáféréssel. Ezek után magamhoz tértem, és tovább keresgélve az open-access.hu oldalon a hírek között szerepel, hogy az OTKA elméletben tényleg bevezette a nyílt hozzáférést.
A kutatási eredmény hasznosítása, publikálása során fel kell tüntetni, hogy az OTKA támogatási szerződés alapján jött létre, és a közleményben meg kell adni az OTKA-szerződés nyilvántartási számát. Az OTKA-támogatással létrejött tudományos közleményt a Nyílt Hozzáférés (Open Access) normái szerint térítésmentesen olvashatóvá kell tenni, vagy a közlés során a szabad olvashatóság jogának biztosításával vagy a közlemény megjelenését követően annak nyilvános hozzáférésű repozitóriumba való elhelyezésével. Az elhelyezés történhet intézményi vagy tudományterületi repozitóriumban, illetve az MTA Könyvtárának Repozitóriumában – REAL: http://real.mtak.hu/
A REAL adatbázisban van egyébként egy jó összefoglaló kezdőknek Holl Andrástól a témakörről, és arról, hogy mit, hogyan, hova.
Tags: hunor, magyarország, nyílt hozzáférés, oa, open access, otka
processing, pt 1
Posted by razor | Filed under English, processing
A while ago I started learning Processing, but I had to stop it because of the spanish exam and various annoying work related stuff. Now I have some time, and also had an idea I wanted to implement. I came up with it after visiting the site of Kitchen Budapest, and besides seeing some cool shit, I also ran into lots junk called [digital] art, and said ‘fuck, I can do better’. I was also inspired by a Processing webcam application. So this will be my notebook on that ‘art project’.
First I wanted a working video capture device in Processing. I had to install Quicktime, because Processing uses Quicktime for Java for video related stuff, displaying QT videos, grabbing video data from cameras [including webcams], etc. As my Dell webcam doesn’t support Quicktime, I also had to install a VDIG, a Quicktime compatible video digitizer. The original WinVDIG site is dead, but a mirror is available here, with the recommended 1.0.1 version. Video capturing almost worked by then, I just had to start Processing in WinXP compatibility mode.
Tested the system with this very complicated script.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 | import processing.video.*; Capture myCapture; void setup() { size(200, 200); myCapture = new Capture(this, width, height, 30); } void captureEvent(Capture myCapture) { myCapture.read(); } void draw() { image(myCapture, 0, 0); } |
Now I’m trying to test the only freely available Java eye tracking library, LEA. A Java library is supposed to work in Processing, yes? More stuff later.
Tags: digital art, eye tracking, java, processing, webcam
nature.com app
Posted by razor | Filed under English, Szolgáltatás
A new iPhone app for nature.com is available at the iTunes store. The interesting part is that you can access all content freely for a while, as the developers are gathering user feedback. So if you have an iPhone, go for it and download the site (or at least the articles you always wanted, but couldn’t get because of the paywall).
Tags: app, iphone, nature, nature.com, science