From sinhashruti.shruti from gmail.com Wed Dec 3 04:54:19 2008 From: sinhashruti.shruti from gmail.com (S.S) Date: Wed Dec 3 11:23:32 2008 Subject: [Bio-software] can't spawn "megablast Message-ID: <20809864.post@talk.nabble.com> Hi, I have been trying to run megablast on standalone but i'm getting a "can't spawn megablast" error. It does perform BLAST for some queries and then ends with the error. Please help. S.S -- View this message in context: http://www.nabble.com/can%27t-spawn-%22megablast-tp20809864p20809864.html Sent from the Bio.net - Bio-soft mailing list archive at Nabble.com. From sinhashruti.shruti from gmail.com Wed Dec 3 06:47:39 2008 From: sinhashruti.shruti from gmail.com (shruti sinha) Date: Wed Dec 3 11:23:39 2008 Subject: [Bio-software] error: can't spawn megablast Message-ID: <22d0ba8e0812030347ib81420cke75d6d3e069493ac@mail.gmail.com> Hi, I have been trying to run megablast on standalone but i'm getting a "can't spawn megablast" error. It does perform BLAST for some queries and then ends with the error. Please help. S.S From sinhashruti.shruti from gmail.com Wed Dec 3 06:56:31 2008 From: sinhashruti.shruti from gmail.com (S.S) Date: Wed Dec 3 11:23:44 2008 Subject: [Bio-software] can't spawn "megablast Message-ID: <20809864.post@talk.nabble.com> Hi, I have been trying to run megablast on standalone through a perl code i've written but i'm getting an error stating: Can't spawn "megablast -d dm -i D:/Data_eArray/E-Array/CGH_Projects/Drosophila/Chromosomes/chrUextra/chrUextra_query.txt -o D:/Data_eArray/E-Array/CGH_Projects/Drosophila/Chromosomes/chrUextra/chrUextra_BR.txt -m 8": No error at BLAST.pl line 20." It does perform BLAST for some queries and then ends with the error. I have tried running this code with other data, and it works with them. Please help. S.S -- View this message in context: http://www.nabble.com/can%27t-spawn-%22megablast-tp20809864p20809864.html Sent from the Bio.net - Bio-soft mailing list archive at Nabble.com. From staffa from niehs.nih.gov Thu Dec 11 10:28:30 2008 From: staffa from niehs.nih.gov (Staffa, Nick (NIH/NIEHS) [C]) Date: Thu Dec 11 10:43:20 2008 Subject: [Bio-software] RE: [Info-gcg] Other: Re - GCG non-support In-Reply-To: <20081103121427.E74728@epsilon.bio.fsu.edu> References: <46B1AEA8.2040308@ebi.ac.uk><20070802081845.D3246@epsilon.bio.fsu.edu><46B2F2E3.4020305@ebi.ac.uk><20070803131050.H7747@epsilon.bio.fsu.edu><1186251135.996351.149470@g12g2000prg.googlegroups.com><46B721F0.8050407@ebi.ac.uk><7930EE6CD7CA354D93B444D0433C061103A8C70D@NIHCESMLBX6.nih.gov><46B83135.7050107@ebi.ac.uk> <20081103121427.E74728@epsilon.bio.fsu.edu> Message-ID: <7930EE6CD7CA354D93B444D0433C061106848CD6@NIHCESMLBX6.nih.gov> I've heard that the legal cost is a measly $70,000. Can we find 70 people to put up $1000? Or 140 to put up $500? Or........ Accelrys is being very wimpy about this; They should give the thing away and let the chips fall where they may. Nickolas G. Staffa, Jr. Ph.D. Telephone: 919-316-4569 (NIEHS: 6-4569) Scientific Computing Support Group NIEHS E-WITS Contract National Institute of Environmental Health Sciences National Institutes of Health Research Triangle Park, North Carolina > -----Original Message----- > From: Steve Thompson [mailto:stevet@bio.fsu.edu] > Sent: Monday, November 03, 2008 3:56 PM > To: Peter Rice > Cc: mol-evol@magpie.bio.indiana.edu; evoldir@evol.biology.McMaster.CA; > bio-soft@magpie.bio.indiana.edu; info-gcg@magpie.bio.indiana.edu; comp- > bio@magpie.bio.indiana.edu > Subject: [Info-gcg] Other: Re - GCG non-support > > Hi Peter - > > I'm picking back up on an old thread from summer 2007 re. the Acclerys GCG > 'retirement.' Since that time several developments, only a few positive > in my opinion, have clarified the situation. > > One - my online petition at www.petitiononline.com was very successful > (http://bio.fsu.edu/~stevet/Accelrys_petition.pdf) in gathering > signatures, almost 200 in a month, and in fostering international > exposure, as the BioInform article from April 2008 attests > (http://bio.fsu.edu/~stevet/BioInformGCG.pdf). But Accelrys remains > committed to not releasing any GCG code, due to exhorbiant and without > profit legal expense. So be it and understood - we tried. > > Two - Accelryrs did distirbute the 'perpetual' licenses to all valid > license holders that were entitled to it, as I announced in this forum > April 2008, and they worked great, even across multiple nodes in a > cluster. Thany you Accelrys. However . . . > > Three - We (FSU) upgraded our Linux cluster that supports GCG and many > other bioinformatics tools to CentOS version 5. Unfortunately, almost > half of the GCG package now fails due to unresolvable library conflicts > (as I warned would happen - unfortunately sooner than I had hoped). Our > systems operations folk initially thought they could fix this but the > solution has remained ellusive. The affected programs are all the oldest > 'legacy' programs in the package, although some longtime GCG pragrams like > Pearson's FastA package remain viable. > > Four - SeqLab continues to operate just fine, but without access to many > of the analytic tools of the package, its usefullness is quite impacted, > though I still think it's one of the best multiple sequence alignment > editors around. This is where you come back in Peter. It may seem odd to > ask, but the need is actually larger now that so much of the package no > longer works in an Enterprise (or CentOS) Linux version 5 environment. > I'm sure that I am not alone in this situation. So here goes - I've asked > it many time before, and I've begun to do the work myself starting with > PlotCon, but has anybody built SeqLab extension configuration files to > launch EMBOSS programs? > > Cheers - Steve > Steven M. Thompson > A C T G stevet@bio.fsu.edu > \-/ > http://bio.fsu.edu/~stevet/cv.html > /\ > /--| FSU SCS / BioInfo 4U > /---/ > |--/ Florida State University School > of > \-/ Computational Science > /\ > /--\ 1st floor DIRAC 150G > |---\ Tallahassee, Florida > \---\ 32306-4120 > \--| 850-644-4490 > \-/ > /\ 2538 Winnwood Circle > /--\ Valdosta, Georgia > /---| 31601-7953 > |--/ 229-249-9751 > > _______________________________________________ > Info-gcg mailing list > Info-gcg@net.bio.net > http://www.bio.net/biomail/listinfo/info-gcg From nir from rosettadesigngroup.com Sat Dec 20 04:01:59 2008 From: nir from rosettadesigngroup.com (Nir London) Date: Sat Dec 20 13:32:50 2008 Subject: [Bio-software] Protein design using ROSETTA Message-ID: An interesting example for the usage of the ROSETTA protein modeling software: http://rosettadesigngroup.com/blog/?p=151 Nir London. Rosetta Design Group http://rosettadesigngroup.com/ From Heather.Vincent from manchester.ac.uk Mon Dec 29 11:12:56 2008 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Mon Dec 29 13:19:41 2008 Subject: [Bio-software] Introduction to Bioinformatics, March 2009 Message-ID: <4958F708.6060405@manchester.ac.uk> The online course 'Introduction to Bioinformatics', from The University of Manchester, will begin again in March 2009. Like all our distance courses it is delivered in a Virtual Learning Environment, which allows us to extend the classroom into the web. We use a range of tools to support our online teaching activities. Each course, which is paced to suit those in full-time employment, runs over 16 teaching weeks. Teaching and learning are focussed around tutor-supported exercises. In this course, participants work together on the interpretation of their results, before receiving feedback from the course tutor. Participants who wish to be assessed for credits at Masters level should complete additional independent research for assessment. Week 1 Introduction to distance learning Bioinformatics as a knowledge-based discipline Weeks 2 and 3 Introduction to the sequence databases Quality, redundancy and annotation Sequence retrieval exercise and group discussion Weeks 4 and 5 Nucleic acid sequence analysis Weeks 6 and 7 Independent research and assessment Weeks 8 and 9 Sequence alignment and database search 1. use of BLAST and FASTA, choosing suitable options; 2. interpretation of the results. Weeks 10 and 11 Protein function prediction. Weeks 12 and 13 Protein structure prediction Practical exercise and group discussion Weeks 14 to 16 Independent research and work on the second assessment You will find information on all our courses, including fees and a link to the online application form, here : http://octette.cs.man.ac.uk/bioinformatics/index.html If you have any questions, or need advice on the module options, please contact Heather.Vincent@manchester.ac.uk