From Patrick_member from newsguy.com Wed Jul 2 23:40:19 2008 From: Patrick_member from newsguy.com (Patrick Flaherty) Date: Thu Jul 3 11:57:19 2008 Subject: [Bio-software] BLAST software Message-ID: Hi - experienced programmer curious about bioinformatics. The BLAST software package seems to figure in prominently. Have looked it up and read some about it (and I'm already familiar with most of the biology that gets mentioned in the context of BLAST). Is it fair to say(hopefully not a gross oversimplification) that the BLAST software might be construed, in some sense, as string matching? If so, then I would assume that algorithms that speed up string matching might also speed up BLAST? I'm sure a great many researchers and bioinformaticians have looked at this issue a great deal (speeding up BLAST - although the trade-off seems to be the exactness of the matches), but I've had my own experience in looking at/using/experimenting with many different approaches to string matching. thanx - pat From Federica.MANUCCI from dit.ie Thu Jul 3 10:23:59 2008 From: Federica.MANUCCI from dit.ie (Federica Manucci) Date: Thu Jul 3 11:57:56 2008 Subject: [Bio-software] Enzyme kinetics calculator Message-ID: <3346.147.252.184.129.1215098639.squirrel@squirrelmail.dit.ie> Dear Mr. or Madame, the reason why I am writing is because I am interested in downloading the Enzyme kinetics calculator for research pourpose. However, in the website I cannot have access to it though the link of the following webpage: http://www.bio.net/bionet/mm/bionews/1997-October/004143.html Can you send me the exact IP address to download it, please? I am looking forward to hearing news from you as soon as possible. Yours faithfully, Federica Manucci Federica Manucci PhD student at Dublin Institute of Technology Cathal Brugha Street Dublin 1 Ireland Mobile ph. 0035 3873223673 Laboratory ph. 0035 31 402 4511 Office ph. 0035 31 402 7541 This message has been scanned for content and viruses by the DIT Information Services E-Mail Scanning Service, and is believed to be clean. http://www.dit.ie From francis from oicr.on.ca Thu Jul 3 08:53:59 2008 From: francis from oicr.on.ca (Francis Ouellette) Date: Thu Jul 3 11:58:02 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7 In-Reply-To: Message-ID: It took some digging (and asking at blast-help@ncbi.nlm.nih.gov), but here is what I got: > It's listed among the amino acids at > http://www.ncbi.nlm.nih.gov/IEB/ToolBox/SDKDOCS/BIOSEQ.HTML J is "Leu or Ile" (from IUPAC and NCBI) Other "specials" are: B Asp or Asn J Leu or Ile O Pyrrolysine X Undetermined or atypical Z Glu or Gln O is not used in BLOSOM (currently). Cheers, f. -- B.F. Francis Ouellette http://oicr.on.ca/research/ouellette/ We are hiring a "Manager, Web Development": http://tinyurl.com/4dgyuk NextGen sequencing Bioinformatics Workshop: http://tinyurl.com/29ulqj ________________________________ >From: Linlin Yan Date: Fri, 27 Jun 2008 22:03:41 -0400 To: Subject: [Bio-software] Re: Bio-soft Digest, Vol 37, Issue 7 On Jun 28, 1:52 am, "Harianto Tjong" wrote: > I think J=W ( or Trp). > For some purpose, amino acids are coded into the first 20 letters of > alphabet, so after the 20th in alphabetical order (T=Threonine), there are > 3 amino acids need to be mapped to fit: V,W,Y into B,J,O (for Val, Trp, > Tyr). I'm afraid the map may be wrong. Usually B means Asp or Asn, but not Val. I haven't seen J or O letter before I found J in NCBI scoring matrix. I guess Raoul Fleckman must be right: J means Leu or Ile. Need to be reassured. > Maybe others can correct me if I'm wrong. > > On Fri, Jun 27, 2008 at 1:03 PM, > wrote: > > > > > Send Bio-soft mailing list submissions to > > bio-s...@net.bio.net > > > To subscribe or unsubscribe via the World Wide Web, visit > > http://www.bio.net/biomail/listinfo/bio-soft > > or, via email, send a message with subject or body 'help' to > > bio-soft-requ...@net.bio.net > > > You can reach the person managing the list at > > bio-soft-ow...@net.bio.net > > > When replying, please edit your Subject line so it is more specific > > than "Re: Contents of Bio-soft digest..." > > > Today's Topics: > > > 1. Re: Which amino acid residue does the letter 'J' mean? > > (Raoul Fleckman) > > > ---------------------------------------------------------------------- > > > Message: 1 > > Date: Thu, 26 Jun 2008 17:34:55 -0500 > > From: Raoul Fleckman > > Subject: [Bio-software] Re: Which amino acid residue does the letter > > 'J' mean? > > To: bionet-softw...@net.bio.net > > Message-ID: > > > Leucine or Isoleucine > > > On 2008-06-25, Linlin Yan wrote: > > > I just found there is a letter 'J' in NCBI's scoring matrix file > > > (e.g. /usr/share/ncbi/data/BLOSUM50). Does anybody know what it is? > > > Thanks! > > -- > Harianto Tjong > 419 IMB > Florida State University > Tallahassee, FL 32306 > Tel : (850) 645-1334 > Fax : (850) 644-7244http://people.scs.fsu.edu/~harianto _______________________________________________ Bio-soft mailing list Bio-soft@net.bio.net http://www.bio.net/biomail/listinfo/bio-soft From yanlinlin82 from gmail.com Fri Jul 4 03:17:05 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Fri Jul 4 10:45:08 2008 Subject: [Bio-software] Re: BLAST software References: Message-ID: On Jul 3, 12:40?pm, Patrick Flaherty wrote: > Hi - experienced programmer curious about bioinformatics. > > The BLAST software package seems to figure in prominently. ?Have looked it up > and read some about it (and I'm already familiar with most of the biology that > gets mentioned in the context of BLAST). > > Is it fair to say(hopefully not a gross oversimplification) that the BLAST > software might be construed, in some sense, as string matching? > > If so, then I would assume that algorithms that speed up string matching might > also speed up BLAST? ?I'm sure a great many researchers and bioinformaticians > have looked at this issue a great deal (speeding up BLAST - although the > trade-off seems to be the exactness of the matches), but I've had my own > experience in looking at/using/experimenting with many different approaches to > string matching. > > thanx - pat In my opinion, there are differences between BLAST and pure string matching. String matching do search text literally, without considering the letter replacing/inserting/deleting probabilities, which may have significance in biology. From yanlinlin82 from gmail.com Fri Jul 4 03:34:15 2008 From: yanlinlin82 from gmail.com (Linlin Yan) Date: Fri Jul 4 10:45:29 2008 Subject: [Bio-software] Re: Enzyme kinetics calculator References: Message-ID: <62085254-cf36-4adf-909c-512ba8561f92@w8g2000prd.googlegroups.com> On Jul 3, 11:23?pm, "Federica Manucci" wrote: > Dear Mr. or Madame, > > the reason why I am writing is because I am interested in downloading the > Enzyme kinetics calculator for research pourpose. However, in the website > I cannot have access to it though the link of the following webpage: > > http://www.bio.net/bionet/mm/bionews/1997-October/004143.html > > Can you send me the exact IP address to download it, please? > > I am looking forward to hearing news from you as soon as possible. > > Yours faithfully, > > Federica Manucci > > Federica Manucci > PhD student at Dublin Institute of Technology > Cathal Brugha Street > Dublin 1 > Ireland > > Mobile ph. 0035 3873223673 > Laboratory ph. 0035 31 402 4511 > Office ph. 0035 31 402 7541 > > This message has been scanned for content and viruses by the DIT Information Services E-Mail Scanning Service, and is believed to be clean.http://www.dit.ie Since it is a excel file writing in or before 1997, it must be deleted or moved to another place. Do you know if there is any software else could do the same calculating for you? From rakesh.shardiwal from gmail.com Sat Jul 5 04:08:48 2008 From: rakesh.shardiwal from gmail.com (SMU_bioinformatics Team) Date: Sat Jul 5 11:27:22 2008 Subject: [Bio-software] You are invited to join our panel of SMU_Bioinformatics expert Message-ID: <94f17b32-1f32-4b97-9d66-5f4505e3c9bb@d77g2000hsb.googlegroups.com> New Website for Bioinformatics You are invited to join our panel of SMU_Bioinformatics experts to create a new live, pioneering, educational and innovative informative website for the Bioinfo & Biotechno students, professionals and researchers. We will be serving the currents trends of research topics, community to share the novel ideas and a virtual Practical session and the free books, tools, jobs requirements etc. Understanding Bioinformatics base, structure, jobs profiles will be the easy and you can submit your questions to our experts. We need your help to understand the user requirements, accessibility and the most important help to gather the resources. If any one is interesting in this project please requested to mail us on smu.bioinformatics@gmail.com and Reply of this message with yes I am interested with Participants name Thank you, Team SMU_Bioinformatics From a.grinyer from sky.com Thu Jul 10 16:32:22 2008 From: a.grinyer from sky.com (Ant Grinyer) Date: Thu Jul 10 19:53:10 2008 Subject: [Bio-software] Call for participation: What types of organisations adopt agile methods? Message-ID: <48767fda.7304843@nntp.motzarella.org> Having worked in software development for over 15 years in many organisations using different development methodologies such as waterfall, RUP, Scrum and XP, I'm still not sure if there is a specific 'type' of organisation that is more likely to adopt agile approaches than others? I guess it could be argued that those organisations that are more innovative or open to change are more likely to adopt agile methods? To try and gain more understanding, and because I have a passion for software development methodologies, I started a PhD five years ago (part-time) to look at this issue. I'm now at the point where I'm conducting a short survey to determine what factors might or might not influence the adoption of agile methods, in the hope to provide some enlightenment. If we get enough participation, I then hope to report this back to the group to see if there are indeed any trends. The survey is short and should take around 5 - 10 minutes to complete, so please bare with the scaled questions whereby you are asked to rate your agreement against a list of statements. To participate, could I kindly ask you to fill in the survey using the link below - http://ou1211237011.agile-adoption.sgizmo.com I believe if we can determine the characteristics of organisations that adopt and do not adopt agile methods, we can get a better understanding whether certain organisations are more conducive to adopting agile methods? Note this is NOT a marketing survey and is used for doctoral and practitioner research purposes. All findings and results will be published to the group and responses treated in strict confidence. Evidence of my research can be found here: http://www.computing.open.ac.uk/PublicWeb/computing/website/people.nsf/(httpPeopleByDepartment)/0843ABBB7405FB3980257439004E6A1F?OpenDocument&subsection=computing Your participation is greatly appreciated. Kindest Regards Ant Grinyer ---------- Business Analyst | Cegedim Pharmaceutical Solutions, UK PhD Candidate | The Open University | Milton Keynes, UK From coelho from ufs.br Sun Jul 13 06:19:21 2008 From: coelho from ufs.br (Diego de Freitas Coelho) Date: Sun Jul 13 13:55:25 2008 Subject: [Bio-software] Biostat B Message-ID: <5d11f8be0807130419x7e4bf59ep389f7f501ed5e599@mail.gmail.com> Hi Mikkel, i'm with your software and acquire a rs-232 to usb cable. but i can't buy a rs-232 to rs-422 converter, because is not disponible in my region.. I would like of the known if i can to use the Biostat B directly with a rs-232 port . or if you know a mode for build a homemade conversor. -- Atenciosamente, Diego de Freitas Coelho Estudante de Qu?mica Industrial UFS - Universidade Federal de Sergipe DEQ - Departamento de Engenharia Qu?mica (79) - 8807-6882 From pritam from thesheltercompany.com Wed Jul 16 03:22:53 2008 From: pritam from thesheltercompany.com (Pritam) Date: Wed Jul 16 08:43:56 2008 Subject: [Bio-software] Need Help Finding Membrane Structure Prediction Software Message-ID: <000001c8e71d$2578ca00$706a5e00$@com> Hello sir/madam, This is pritam gupta from Singapore. I am doing more on membrane structure. I am looking for a software which can give me membrane properties, patterning, analysis and other facilities.plz suggest me to solve my problem. Best regards pritam From giuseppe.salemi from unipd.it Wed Jul 16 02:58:10 2008 From: giuseppe.salemi from unipd.it (Giuseppe Salemi) Date: Wed Jul 16 08:44:02 2008 Subject: [Bio-software] SOFTWARE SANTIS 1.1 for time series and signal analysis Message-ID: <002901c8e719$b0b17e40$5541a293@Lrg15> Dear Sirs, where I can download this package and the user manual? Thank you in advance for your time and cooperation Prof. Giuseppe Salemi Universit? di Padova DAUR - LRG From engelbert_buxbaum from hotmail.com Wed Jul 16 10:51:17 2008 From: engelbert_buxbaum from hotmail.com (Dr Engelbert Buxbaum) Date: Wed Jul 16 13:16:17 2008 Subject: [Bio-software] Re: Need Help Finding Membrane Structure Prediction Software References: Message-ID: Am 16.07.2008, 04:22 Uhr, schrieb Pritam : > Hello sir/madam, > > This is pritam gupta from Singapore. I am doing more on membrane > structure. > I am looking for a software which can give me membrane properties, > patterning, analysis and other facilities.plz suggest me to solve my > problem. What properties or patterns are you looking for? From db60 from st-andrews.ac.uk Thu Jul 17 11:13:17 2008 From: db60 from st-andrews.ac.uk (Daniel Barker) Date: Thu Jul 17 11:12:11 2008 Subject: [Bio-software] bms_runner 1.2 Release Message-ID: Dear all, bms_runner is free software to predict functional linkage among gene products, on the basis of correlated gain and loss of genes from genomes (Barker et al. 2007). It does this by helping the user to configure and repeatedly launch the separate BayesTraits program (Pagel et al. 2004). bms_runner version 1.2 has just been released, with important improvements. bms_runner works under Linux or Mac OS X. It may be downloaded here: http://biology.st-andrews.ac.uk/cegg/software.html I will be happy to receive any questions and feedback on bms_runner. References: Barker et al. 2007, http://dx.doi.org/10.1093/bioinformatics/btl558 Pagel et al. 2004, http://dx.doi.org/10.1080/10635150490522232 Best regards, Daniel -- Daniel Barker http://bio.st-andrews.ac.uk/staff/db60.htm The University of St Andrews is a charity registered in Scotland : No SC013532 From joyjoy.nt from gmail.com Mon Jul 21 04:36:15 2008 From: joyjoy.nt from gmail.com (Jyothish NT) Date: Mon Jul 21 06:34:02 2008 Subject: [Bio-software] Software needed... In-Reply-To: References: Message-ID: Hi all, Can you please suggest some comercial softwares that can help me Molecular modelling Datamining Support Vector Machine Neural Networks. -- Regards... Jyothish N.T. Research Assistant 116, Dept. of Mathematics, Indian Institute of Technology Bombay, Powai, Mumbai-400076. Email : jyothish@iitb.ac.in Ph : +91-9920980148 From barton.michael from gmail.com Mon Jul 21 06:06:17 2008 From: barton.michael from gmail.com (Mike Barton) Date: Mon Jul 21 11:17:04 2008 Subject: [Bio-software] Bioinformatics Survey Message-ID: Hi, I'm trying to get some data on pursuing a career in bioinformatics, and if you have a spare five minutes could you take the time to answer some the questions? You can leave any fields blank that you don't wish to answer. The link is here. http://www.bioinformaticszen.com/2008/07/creating-a-picture-of-different-careers-in-bioinformatics/ Thanks Michael Barton From amit.p from ocimumbio.com Mon Jul 21 23:38:18 2008 From: amit.p from ocimumbio.com (Amit Dattatreya Parhar) Date: Tue Jul 22 08:17:40 2008 Subject: [Bio-software] Re: Bio-soft Digest, Vol 38, Issue 8 References: <200807211703.m6LH3bO07587@net.bio.net> Message-ID: <008d01c8ebb4$c6700590$fc02a8c0@ocimumbio.net> Dear Jyothish Hi all, > > Can you please suggest some comercial softwares that can help me > > Molecular modelling > Datamining > Support Vector Machine > Neural Networks. > FOr SVM you can use libSVM, winSVM http://www.csie.ntu.edu.tw/~cjlin/libsvm/ for free. For molecular modelling : you opt for expensive http://accelrys.com/products/discovery-studio/ or you can go for cheaper and effective : http://www.yasara.org/ For datamining there is nothing better than R-package which is absolutely free and very good. but you have to install and learn its commands to use. If your lab is doing microarrays experiments then you should opt for http://www.ocimumbio.com/web/bioinformatics/prod_details.asp?prod_id=20&prodType=1 regards, Amit ----- Original Message ----- From: To: Sent: Monday, July 21, 2008 10:33 PM Subject: Bio-soft Digest, Vol 38, Issue 8 > Send Bio-soft mailing list submissions to > bio-soft@net.bio.net > > To subscribe or unsubscribe via the World Wide Web, visit > http://www.bio.net/biomail/listinfo/bio-soft > or, via email, send a message with subject or body 'help' to > bio-soft-request@net.bio.net > > You can reach the person managing the list at > bio-soft-owner@net.bio.net > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Bio-soft digest..." > > > Today's Topics: > > 1. Software needed... (Jyothish NT) > 2. Bioinformatics Survey (Mike Barton) > 3. Re: Software needed... (Stephen Wolstenholme) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Mon, 21 Jul 2008 15:06:15 +0530 > From: "Jyothish NT" > Subject: [Bio-software] Software needed... > To: bio-soft@magpie.bio.indiana.edu > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > Can you please suggest some comercial softwares that can help me > > Molecular modelling > Datamining > Support Vector Machine > Neural Networks. > > > -- > Regards... > Jyothish N.T. > Research Assistant > 116, Dept. of Mathematics, > Indian Institute of Technology Bombay, > Powai, Mumbai-400076. > > Email : jyothish@iitb.ac.in > Ph : +91-9920980148 > > > ------------------------------ > > Message: 2 > Date: Mon, 21 Jul 2008 04:06:17 -0700 (PDT) > From: Mike Barton > Subject: [Bio-software] Bioinformatics Survey > To: bionet-software@moderators.isc.org > Message-ID: > > Content-Type: text/plain; charset=ISO-8859-1 > > Hi, > > I'm trying to get some data on pursuing a career in bioinformatics, > and if you have a spare five minutes could you take the time to answer > some the questions? You can leave any fields blank that you don't wish > to answer. > > The link is here. > > http://www.bioinformaticszen.com/2008/07/creating-a-picture-of-different-careers-in-bioinformatics/ > > Thanks > > Michael Barton > > > > ------------------------------ > > Message: 3 > Date: Mon, 21 Jul 2008 13:01:29 +0100 > From: Stephen Wolstenholme > Subject: [Bio-software] Re: Software needed... > To: bionet-software@moderators.isc.org > Message-ID: > Content-Type: text/plain; charset=us-ascii > > On Mon, 21 Jul 2008 15:06:15 +0530, "Jyothish NT" > wrote: > > >Hi all, > > > >Can you please suggest some comercial softwares that can help me > > > >Molecular modelling > >Datamining > >Support Vector Machine > >Neural Networks. > > You can try my EasyNN-plus and SwingNN for free. > > Steve > > -- > EasyNN-plus. Build Neural Networks. http://www.easynn.com > SwingNN. Forecast the Future. http://www.swingnn.com > Neural Planner Software Ltd http://www.NPSL1.com > > > > ------------------------------ > > _______________________________________________ > Bio-soft mailing list > Bio-soft@net.bio.net > http://www.bio.net/biomail/listinfo/bio-soft > > End of Bio-soft Digest, Vol 38, Issue 8 > *************************************** From Rob.Reedijk from douglasconnect.com Wed Jul 23 16:52:04 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Jul 23 16:55:20 2008 Subject: [Bio-software] CFP, Bursary Awards; Life Sciences Innovation, Knowledge Management, Drug Discovery Informatics Message-ID: <892f4c6b-afd3-402e-8e26-334d46ea1673@m45g2000hsb.googlegroups.com> I am posting details for the InnovationWell Autumn Community of Practice Meeting in October 2008 in Bryn Mawr, Philadelphia. Please note that the deadline to apply for bursaries is July 31, 2008. Innovation in Life Science & Healthcare Research and Product Development InnovationWell Autumn Community of Practice Meeting October 14-17, 2008 Bryn Mawr College, Bryn Mawr, Philadelphia, USA Conference Link: http://innovationwell.net/comty_conferences The InnovationWell program will be covering topics in systems biology, computational biology, knowledge management, translational medicine, metabolomics, and predictive toxicology. The eCheminfo program will be covering topics in drug discovery informatics. Abstracts (300-500 words) should be submitted to innovationwell -[at]- douglasconnect.com or echeminfo -[at]- douglasconnect.com by 31 July 2008, and be accompanied by a short biography of the presenting author (300-500 words). Abstracts approved by the scientific organizing committee will be selected for scheduling on the conference program and in meeting poster sessions. Authors will be notified of acceptance as soon as a review of submitted materials takes place and at the latest by 15 August 2008. Bursary Award Bursary Awards will be used to support the attendance of a selection of academic young investigators at the meeting and workshops. Applicants can be working in any area of research related to drug discovery & development at the postdoctoral, graduate student and senior undergraduate levels. To apply for the bursary please send an email with a) your abstract and biography (300-500 words each), b) your CV of 1-2 pages, c) a short description of your interests and career motivations(300-500 words) to innovationwell -[at]- douglasconnect.com or echeminfo -[at]- douglasconnect.com by 31 July 2008. The recipients of the bursary awards will be selected based on an evaluation of the quality and innovation of the described research and the potential positive impact of attendance at the meeting on their research and career progress. Authors will be notified of acceptance by 15 August 2008. We gratefully acknowledge the sponsorship support of the Chemical Computing Group, Merck Research Laboratories, SimBioSys, Tibotec, Tripos and MEDIT. More information at: InnovationWell Program http://innovationwell.net/COMTY_conferences http://innovationwell-bm810.eventsbot.com/ eCheminfo Program http://echeminfo.com/COMTY_conferences http://echeminfoBM810.eventsbot.com Rob Reedijk InnovationWell Community of Practices From Mike.Fursov from gmail.com Fri Jul 25 10:03:42 2008 From: Mike.Fursov from gmail.com (Mikhail Fursov) Date: Fri Jul 25 11:21:05 2008 Subject: [Bio-software] UGENE v1.1 released Message-ID: <60a09693-bef1-41a6-b7be-9ef1479339a2@j1g2000prb.googlegroups.com> About: UGENE is a free software aimed to integrate most of the important molecular biology tools within a single graphical environment that runs fast both on Linux and Windows systems and is able to utilize resources of modern multi-core hardware. Some of new features in version 1.1: * Graphical interface and integration of HMMER2 command line tools. * Support for gzipped data files ... The complete list of features is available here: http://ugene.unipro.ru/changelist.html Link: http://ugene.unipro.ru