From Glenn.Odell from cwine.com Mon Aug 4 18:58:09 2008 From: Glenn.Odell from cwine.com (Glenn.Odell@cwine.com) Date: Mon Aug 4 19:30:33 2008 Subject: [Bio-software] QC software Message-ID: Dear Sir, I have recently started using MedLabQC for internal QC of analyses within our winery analytical labs. It is very intuitive, flexible and powerful and beats the heck out of coming up with something myself. Getting it for free is almost embarrassing. My organization has several labs and would like to compare, consolidate and report the data between the labs. Is there a version of this software designed to do that? I would certainly be willing to consider justifying a reasonable cost for an enterprise version of the software Thanks Glenn O'Dell Director, Group Quality Improvement Constellation Wines, US (209)365-8024 (office) (209) 471-2802 (cell) glenn.odell@cwine.com From iyerarunv from yahoo.com Thu Aug 7 20:23:18 2008 From: iyerarunv from yahoo.com (arun iyer) Date: Fri Aug 8 11:13:23 2008 Subject: [Bio-software] Clustal percent identity matrix Message-ID: <415267.22669.qm@web50311.mail.re2.yahoo.com> I was wondering if the % identity matrix in clustal is actually useful to?assign an bacteria as a distinct?species. I ran an multiple alignment for DNA using default parameters. the % identity matrix shows that the 2 organisms?is 97% identical. The absoulute nucleotide identity is 99%. the % ID matrix is generated after penalties...but is it really useful? __________________________________________________________ Not happy with your email address?. Get the one you really want - millions of new email addresses available now at Yahoo! http://uk.docs.yahoo.com/ymail/new.html From darek.kedra from gmail.com Tue Aug 12 08:12:23 2008 From: darek.kedra from gmail.com (darked) Date: Tue Aug 12 12:17:09 2008 Subject: [Bio-software] Re: Clustal percent identity matrix References: Message-ID: On Aug 8, 2:23 am, arun iyer wrote: > I was wondering if the % identity matrix in clustal is actually useful to assign an bacteria as a distinct species. > I ran an multiple alignment for DNA using default parameters. the % identity matrix shows that the 2 organisms is 97% identical. The absoulute nucleotide identity is 99%. > the % ID matrix is generated after penalties...but is it really useful? What are your DNA sequences? It does not make sense to speak about % identity without knowing what you compare to what. Human and chimp differ more on nucleotide level among many coding sequences. Two different copies of genome of the same, presumably single organism may differ much more, i.e Ciona. So it all depends darked http://openwetware.org/wiki/Wikiomics From motta632000 from gmail.com Sun Aug 17 19:13:10 2008 From: motta632000 from gmail.com (Mauricy Motta) Date: Sun Aug 17 20:24:15 2008 Subject: [Bio-software] PAGE analysis software. BANDLEADER upgrade Message-ID: <48A8BE96.2010406@gmail.com> Hello Maayan, Plese help me to find a copy of BandLeader for Windows. Thanks in advance, Sincerely M.A.Motta, PhD. From qattan.amal from gmail.com Mon Aug 18 15:06:51 2008 From: qattan.amal from gmail.com (AQ) Date: Mon Aug 18 15:09:05 2008 Subject: [Bio-software] Phosphorylation analysis Message-ID: Dear all, Did any one know If we have the MW 60008.7 Da for protein X, and 3 spectra in +2H and the calculated +1H peptide mass amu was 1,407.71 ,In which way could these information help to identify the modifications ?? From qattan.amal from gmail.com Mon Aug 18 15:19:14 2008 From: qattan.amal from gmail.com (AQ) Date: Mon Aug 18 16:04:27 2008 Subject: [Bio-software] phosphorylation Message-ID: <13c853ad-9cc4-4d8e-b902-ae18cd33ac48@m73g2000hsh.googlegroups.com> Dear all, if we have the MW 60008.7 Da for protein X, and u have 3 spectra in +2H and the calculated +1H peptide mass amu was 1,407.71 ??? In which way could these information help to identify the modifications ?? Thanks alot From orry.molsoft from gmail.com Mon Aug 18 18:18:24 2008 From: orry.molsoft from gmail.com (Andrew Orry) Date: Mon Aug 18 19:54:17 2008 Subject: [Bio-software] Protein Structure and Drug Design Workshop - MolSoft October 2-3 2008 Message-ID: <48AA0340.5060206@molsoft.com> MolSoft ICM Workshop: "Protein Structure and Drug Discovery" October 2nd to 3rd 2008 La Jolla, CA. Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on October 2nd to 3rd 2008 in La Jolla, California USA. See www.molsoft.com/training.html for more information and a registration form. Our workshops are suitable for chemists and biologists who would like to learn more about computational drug discovery and bioinformatics. No prior knowledge in this field is required to participate. The workshop is presented by Prof. Ruben Abagyan (The Scripps Research Institute) and Dr. Maxim Totrov (MolSoft). The workshops will consist of lectures, demonstrations, and "hands-on" computational experiments and will cover the following topics: - Sequence and Protein Structure Analysis - Protein Modeling and Simulations - Structure Validation and Optimization - Ligand Binding Site Prediction - Small Molecule Docking and Virtual Ligand Screening - Structure-based development of target-specific compound libraries - Cheminformatics, chemical clustering, searching, superposition etc - QSAR, machine learning - Protein-Protein Docking We will demonstrate and train you in the use of many of our new developments in computational chemistry and biology including: - 3D Ligand Editor - design and optimize ligands interactively - Markush Library Docking - Multiple Receptor Docking (A method to incorporate receptor flexibility) - Automated model building into electron density - Atomic property field chemical superposition - Fast machine learning tools for QSAR - Pharmacophore drawing and searching - Compound library enumeration tools - Screen-grabbing movie making "The objective of this training workshop is to help chemists and biologists solve challenging problems in the area of drug discovery by efficient use of the science and technology present in ICM molecular modeling tools." Prof. Ruben Abagyan (The Scripps Research Institute and Co-Founder of Molsoft LLC) Please see our website at www.molsoft.com for more details or E mail andy@molsoft.com or call (858) 625 2000 ext.108. Please join the ICM Discussion Forum: http://groups.google.com/group/molsoft-icm-forum Latest Newsletter: http://www.molsoft.com/july08.html MolSoft is a La Jolla based company that is a primary source of new breakthrough technologies in computational chemistry and biology. Molsoft is committed to solving intellectually challenging problems in drug discovery and computational biology. -- Andrew Orry Ph.D. Senior Scientist MolSoft LLC 3366 North Torrey Pines Court Suite 300 La Jolla, CA 92037 U S A Phone: (858) 625-2000 (x108) Fax: (858) 625-2888 www.molsoft.com From dnaresearchcentre from gmail.com Thu Aug 21 03:20:20 2008 From: dnaresearchcentre from gmail.com (Dna research centre) Date: Thu Aug 21 08:07:42 2008 Subject: [Bio-software] Training and Projects Message-ID: DNA RESEARCH CENTRE *HYDERABAD *BHUBANESHWAR *CHANDIGARH DNA RESEARCH CENTRE IS NOW REGISTERED UNDER MINISTRY OF CORPORATE AFFAIRS, GOVT OF INDIA. WE ARE NOW REGISTERED UNDER THE NAME BIOAXIS DNA RESEARCH CENTRE PRIVE LIMITED. WHY DRC? (http://www.dnares.in) *Over 2000 students trained in the year 2008 as of June *Tie up with various national and international universities *Services to Hospitals, Biotech R&D Organizations and Life science sectors *Placement with high profile companies *Unmatched training modules and curriculum *Total R&D Experience in the training session *Students encouraged to work with our Scientists and Researchers on various projects *Paper Publications every month *Maximum updated facilities in DRY and wet labs. *Unmatched courses and course curriculum *Student exchange programs *India’s only lab in Immunoinformatics and among very few labs undertaking private DNA Forensics cases and trainings. *One year membership to every trainee free of cost *Group discounts and scholarships *Membership to different academics and corporate *Industrial and live projects COURSES OFFERED ON (http://dnares.in/trainings.asp) BIOINFORMATICS (30 DAYS, 45 DAYS, 60 DAYS, 90 DAYS, 180 DAYS, 365 DAYS) CHEMIOINFORMATICS (30 DAYS) IMMUNOINFORMATICS (30 DAYS) PHARMACOINFORMATICS AND DRUG DESIGN (45 DAYS) METABOLOMICS (30 DAYS) MEDICAL AND CLINICAL INORMATICS (30 DAYS) RECOMBINANT DNA TECHNOLOGY (15 DAYS, 2MONTHS) IMMUNOTECHNOLOGY (15 DAYS, 2 MONTHS) ENZYMOLOGY (15 DAYS, 2 MONTHS) DNA FORENSICS (45 DAYS) SAS GENOMICS AND CLINICAL TRIALS (30DAYS, 60 DAYS, 120 DAYS) CLIENT SPECIFIC TRAININGS BATCHES STARTING IN 2008 28TH JULY, 11TH AUG, 25TH AUG,8TH SEP, 15TH SEP, 29TH SEP, 6TH 0CT, 20TH OCT, 27TH OCT, 10TH NOV, 24TH NOV, 8TH DEC, 22ND DEC, 29TH DEC REGISTRATION DEADLINES FOR BATCHES UPTO SEPTEMBER EITHER BY POST OR IN PERSON: 23RD OF AUGUST (Till 6:00pm) FOR BATCHES AFTER SEPTEMBER – 15TH OF OCTOBER 2008 (Till 6:00pm) HOW TO REGISTER? (http://dnares.in/online-registration.asp) Please visit the online registration portal of the website www.dnares.in, www.bioaxis.in in the training section. (http://dnares.in/ trainings.asp) If you are interested in us please contact: DRC Hyderabad: +91-40-40180502/09247438983 DRC BBSR: +91-674-6548502/09238338983 DRC Chandigarh: +91-1762-286502/09256280538 Write to us at dnaresearchcentre@gmail.com (national), dnaresearchcentre@yahoo.com (International) From tiagoantao from gmail.com Wed Aug 27 09:37:03 2008 From: tiagoantao from gmail.com (Tiago Antao) Date: Wed Aug 27 10:49:58 2008 Subject: [Bio-software] Easy to use selection detection software Message-ID: <0d841ebd-5dae-42e2-9c19-bfefd341d2b3@2g2000hsn.googlegroups.com> Dear Colleagues, We have developed a easy to use program for selection detection based on the fdist Fst outlier method. The software runs directly from the web, no installation required. The major requirement is a recent version of Java installed (a link can be found on the application site) If you are interested in selection detection using Fst-outlier methods, please check our application, LOSITAN. URL: http://www.biomedcentral.com/1471-2105/9/323 Best Regards From Rob.Reedijk from douglasconnect.com Wed Aug 27 18:33:36 2008 From: Rob.Reedijk from douglasconnect.com (Robby) Date: Wed Aug 27 18:37:41 2008 Subject: [Bio-software] Bursary Award - eCheminfo Community of Practice Workshop, India, December 2008 Message-ID: <60ef0a9d-8403-4d90-9e54-fd889911724d@v57g2000hse.googlegroups.com> I am posting details for the eCheminfo Community of Practice Drug Discovery Design Methods & Applications Workshop Meeting in December 2008 in Hyderabad, India. Please note that the deadline to apply for the bursary is September 12, 2008. Drug Discovery Design Methods & Applications Workshop December 15-18, 2008 IIIT Hyderabad, Hyderabad, India Please visit http://echeminfo.colayer.net/comty_hyderabadworkshop08 Virtual screening, structure-based drug design, lead optimisation and predictive ADME/toxicology supporting decision making in drug discovery a Hands-on eCheminfo Workshop This workshop precedes the “Latest Advances in Drug Discovery Modelling & Informatics” eCheminfo Community of Practice InterAction Meeting December 19-20, 2008 Co-organised in Partnership by IIIT Hyderabad , JNU NewDelhi , Seascape Learning, and Douglas Connect Facilitated by Barry Hardy Work through in detail and discuss practical examples, methods and emerging techniques with leading modelling experts! Virtual Screening & Docking Structure-based Drug Design Ligand Optimisation & Library Design Structure Search, Similarity and Property Estimation Data Mining, Analysis & Visualisation Pharmacophore Modelling for Lead Identification Fragment-based Drug Design Predictive ADME QSAR-based Predictive Toxicology These workshops are aimed to provide a set of stimulating workshops using latest advanced modelling techniques of relevance to chemists, life scientists and modellers working in drug discovery. Participants should return to their labs with new ideas, best practices and software experiences to maximise productivity in their own drug discovery research activities. Workshop groups will study problems with hands-on examples using leading-edge software and discuss complex issues highlighted by examples and case studies presented by instructors. Software packages and an IT classroom will be used by instructors and participants to work through drug discovery and optimisation problems. Participants may propose problems and issues to the faculty ahead of the workshop. Participants will also have ample opportunity to discuss their perspectives and criticisms of the methods studied and should take-away key nuggets of understanding from these intensive sessions. Workshop Leaders Johann Gasteiger (Molecular Networks, Germany), Jeff Wiseman (Locus Pharmaceuticals, USA), Indira Ghosh (JNU, New Delhi, India), Paul Hawkins (OpenEye, USA), Barry Hardy (Douglas Connect, Switzerland), Peter Oledzki (BioSolveIT, Germany), Dhananjay Bhattacharyya (Saha Institute of Nuclear Physics, India), Ismael Zamora (Pompeu Fabra University and Lead Molecular Design, Spain), Wojciech Plonka (Fujitsu Group, Japan), Madhavi Sastry (Schrodinger) A Bursary Award will be used to support the attendance of one academic participant at the workshop. Please visit http://echeminfo.colayer.net/comty_hyderabadworkshop08 For further information and questions on the Workshop program, please contact Dr. Barry Hardy at: barry.hardy -[at]- douglasconnect.com, Tel: +41 61 851 0170 . For international registrations, please contact Nicki Douglas, nicki.douglas –[at]- douglasconnect.com, Tel: +41 61 851 0461 If you are located in India, please contact Sunil Chawla at: sunil - [at] -seascapelearning.com, Tel: +91 981 0305 923 or Om Prakash at Tel: +91 985 0709 150 to complete your registration and payment in Rs. For more information, please visit http://seascapelearning.com/echeminfo_reg.html Rob Reedijk eCheminfo Community of Practice