From mitotyper from gmail.com Mon Aug 3 12:28:31 2009 From: mitotyper from gmail.com (dee) Date: Mon Aug 3 12:44:08 2009 Subject: [Bio-software] Please help to test new mtDNA analysis software Message-ID: <67c02574-e1cc-4b65-a628-c8d5486c8cab@j21g2000yqe.googlegroups.com> Hello Dear Colleagues! We are currently developing a new automating mtDNA analysis software, and are in great need in your competent opinion and feedback. Our team would be really grateful to you, if you could give us some criticism (or maybe even praise). The program currently runs under MS Windows OS and requires Microsoft .net framework 2.0 to be installed on your computer. It works with *.ab1 files and is doing it quite well (as we hope :) ) If you would be so kind to help in testing - please email me to mitotyper@gmail.com for i could send you a license key, or just post your email in reply. Download link is http://rapidshare.com/files/262683748/Mitotyper.msi.html Thank you very much, Alexey. From manuel.cano from cafedecolombia.com Thu Aug 6 09:36:27 2009 From: manuel.cano from cafedecolombia.com (Manuel Cano) Date: Thu Aug 6 10:49:06 2009 Subject: [Bio-software] About Interproscan In-Reply-To: References: Message-ID: Hi Dale, I am Manuel Cano, I work for one of the biggest coffee research centers in Colombia at the Bioinformatics department and now I am trying to install Interproscan in some of the machines we use here, but I am getting an error (which I saw on a forum of yours) when I test it, so I was wondering if you solved the problem and how did you do so? This is the message: pijao:bin sge$ ./iprscan -cli -i ../test.seq -iprlookup -goterms SUBMITTED iprscan-20090806-09271322 FAILED Iprscan job iprscan-20090806-09271322 failed and exit with status code 256 ./iprscan: /Users/sge/opt/iprscan/tmp/20090806/iprscan-20090806-09271322/iprscan-20090806-09271322.xml unavailable : No such file or directory /Users/sge/opt/iprscan/bin/iprscan_wrapper.pl: failed to send error to administrator: no destination address Tool: iprscan JobID: iprscan-20090806-09271322 Time: Thu Aug 6 09:27:13 2009 Error: I would appreciate if you can help me with this because there is not much information about it on the net. Thanks in advance Sincerely -- Manuel Fernando Cano Montes. Systems and Telecommunications Engineer University of Manizales. Alumnus AIESEC Manizales, Colombia Bioinform?tica department Cenicaf? (Centro Nacional de Investigaciones de Caf?) - FNC E-mail: manuel.cano@cafedecolombia.com Tel: +57 3218169084 From Heather.Vincent from manchester.ac.uk Thu Aug 6 11:10:08 2009 From: Heather.Vincent from manchester.ac.uk (Heather Vincent) Date: Thu Aug 6 11:13:05 2009 Subject: [Bio-software] Introduction to Bioinformatics, October 2009 Message-ID: <4A7B0060.3000805@manchester.ac.uk> The online course, Introduction to Bioinformatics, from The University of Manchester, will begin again in October 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. 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 From sanjaysingh765 from gmail.com Sat Aug 15 07:07:06 2009 From: sanjaysingh765 from gmail.com (chunnu) Date: Sat Aug 15 12:29:33 2009 Subject: [Bio-software] batch query Message-ID: Hi there, i want to use BLINK at NCBI in batch query mode. Does anybody has perlscript to do so. I would be very grateful if soomeone share it with me. regards sanjay From leach from MIT.EDU Thu Aug 20 10:46:05 2009 From: leach from MIT.EDU (Alexander Leach) Date: Thu Aug 20 11:38:38 2009 Subject: [Bio-software] Scientific Dictionary for MS Word Message-ID: <1250783172.24fFDEa3.2702818DF421954E02C4FB7743E874F8BD52AF6450C@EXPO9.exchange.mit.edu> Hi, I came across a forum article written in 1996 saying that you are working on a Microsoft Word dictionary for biologists, having already made one for "chemistry and biochemistry, and organic.". I don't suppose you've done this and can forward me a copy, please?? Actually a generic "scientist" dictionary would be ideal for me, as I did my initial degree in (Joint Honours) Chemistry & Physics, and now do computational biology. The article I found is here:- http://www.bio.net/bionet/mm/bio-soft/1996-April/014002.html What's the chances you don't use this e-mail address any more....? :( I'd really appreciate it, for reasons I'm sure you already know and can relate with! Kind regards, Alex Leach