Hello, I'm sysadmin at European Molecular Biology Laboratory (EMBL), Grenoble. After the "Debian for Scientific Facilities Days" that took place on June, 24-26 at ESRF where we met Andreas ; we decided to work with the Debian Med Blend to package and include in the offical Debian archive some electron microscopy softs that our users are using. Currently they use this list of software: - AMoRe (http://mem.ibs.fr/JORGE/index.html ) - atsas (EMBL Hamburg, not sure we can re-distribute it) - blast (not sure if it's a former version of the package blast2 that already exists in debian) - bsoft (http://lsbr.niams.nih.gov/bsoft/ ) - chimera (http://www.cgl.ucsf.edu/chimera/ ) - coot (http://lmb.bioch.ox.ac.uk/coot/ ) - ctfind3 and ctftilt (http://emlab.rose2.brandeis.edu/ctf ) (GPLv3) - eman2 (http://blake.bcm.edu/emanwiki/ ) - embfactor (https://sites.google.com/site/3demimageprocessing/embfactor ) - empft/em3dr (http://bilbo.bio.purdue.edu/~viruswww/Rossmann_home/softwares/river_programs/para-pft-em3dr.php ) - flex-em (http://salilab.org/Flex-EM/ ) - frealign (http://emlab.rose2.brandeis.edu/frealign ) (GPLv3) - image2000 (http://www2.mrc-lmb.cam.ac.uk/image2000.html ) - imagic (http://www.imagescience.de/imagic.html ) - imod (http://bio3d.colorado.edu/imod/ ) - maloc (http://fetk.org/codes/maloc/ ) - modeller (http://salilab.org/modeller/ ) - naccess (http://www.bioinf.manchester.ac.uk/naccess/ ) - nuccyl (http://www.biosci.ki.se/groups/ljo/software/nuccyl.html ) - peet (http://bio3d.colorado.edu/PEET/ ) - relion (http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page ) - Rico (http://mem.ibs.fr/JORGE/index.html ) - saxsview (http://saxsview.sourceforge.net/ ) - spider (http://www.wadsworth.org/spider_doc/spider/docs/spider.html ) - tiltpicker (http://www.ncbi.nlm.nih.gov/pubmed/19374019 ) - uro (http://mem.ibs.fr/JORGE/index.html ) - veda (http://mem.ibs.fr/GAEL/ ) - vmd (http://www.ks.uiuc.edu/Research/vmd/ ) - xmipp (http://xmipp.cnb.csic.es/twiki/bin/view/Xmipp/WebHome ) - zdock (http://zlab.umassmed.edu/zdock/ ) Most used at EMBL Grenoble are spider, xmipp and eman2. I already packaged Xmipp 3.0 on wheezy, but I can't compile it on squeeze as it needs python-numpy >= 1.6 which is not available even in squeeze-backports . I also made a package for spider, but it's not very clean yet... I worked with the developer to make it compile with gfortran and not only with PGI or ifort. My co-worker is currently working on ctfind and ctftilt. The main problem we encountered so far is that that kind of program often lack of clean Makefile and have non traditional install procedure (./configure && make && make install), so we have to write it first... We may not have a lot of time to dedicate to packaging in the next few weeks, but we'll try to get a few software in Debian Med before the end of the year. I'd like to know how we can start working with Debian Med (include list of software on this page: http://debian-med.alioth.debian.org/tasks/bio , upload unofficial packages for review, become a member of the debian med team...) and if some of you is using one of the softs we use. Regards, Mickaël
Attachment:
signature.asc
Description: This is a digitally signed message part