From novalidaddress from nurfuerspam.de Thu Jan 1 08:33:38 2009 From: novalidaddress from nurfuerspam.de (WS) Date: Thu Jan 1 12:00:25 2009 Subject: [Bio-software] Make Akta Prime Software work under Linux!? Message-ID: <15826fa4-7f63-4597-a045-2cc4f5ec2983@z28g2000prd.googlegroups.com> Dear Colleagues, I am about to make the ?kta Prime package run with Opensuse Linux 11.1 (WINE 1.1.9, Kernel 2.6.27.7-9-default). I already successfully have set up the Prime software to acquire data from the machine (for monitoring runs, "Csyscon.exe prime"). However, I have serious problems doing the same with the Evaluation software ("Emain.exe prime") that is used to analyze the data. Currently, I am figthing with DLLs (MFC42.DLL and MSVCRT.DLL in detail) as I get error messages pointing to unresolved functions, the app crashed after loading any data set. I already have tried all versions of these DLLs I could get hold of, but no success yet. Has anyone already solved the "problem" or wants to do the same and is willing to share her/his experience? Or is interested to team up? Best regards, Wolfgang (?kta/Akta Prime is an FPLC protein purification machine from Pharmacia/Amersham/GE-Healthcare) From ddloeb from gmail.com Fri Jan 2 12:45:29 2009 From: ddloeb from gmail.com (ddloeb@gmail.com) Date: Fri Jan 2 13:10:37 2009 Subject: [Bio-software] Re: Make Akta Prime Software work under Linux!? References: Message-ID: <815d5159-4fe1-4c5a-9009-1fd9c07fe372@r36g2000prf.googlegroups.com> On Jan 1, 7:33?am, WS wrote: > Dear Colleagues, > > I am about to make the ?kta Prime package run with Opensuse Linux 11.1 > (WINE 1.1.9, Kernel 2.6.27.7-9-default). I already successfully have > set up the Prime software to acquire data from the machine (for > monitoring runs, "Csyscon.exe prime"). However, I have serious > problems doing the same with the Evaluation software ("Emain.exe > prime") that is used to analyze the data. Currently, I am figthing > with DLLs (MFC42.DLL and MSVCRT.DLL in detail) as I get error messages > pointing to unresolved functions, the app crashed after loading any > data set. I already have tried all versions of these DLLs I could get > hold of, but no success yet. I don't use Akta Prime (or Wine), but in general I have three suggestions: a) Have you tried Codeweavers Crossover-Linux? It is based on Wine, but is compatible with more Windows applications than Wine is. b) I use VMWare - haven't found a single application that doesn't work with it yet. But then again, they're running in a Windows XP guest session running on Linux. c) You could try Bochs. It is a little slower than VMWare - differences in virtualization routines, but Bochs is free Dan From novalidaddress from nurfuerspam.de Sat Jan 3 05:46:14 2009 From: novalidaddress from nurfuerspam.de (WS) Date: Sat Jan 3 13:55:10 2009 Subject: [Bio-software] Re: Make Akta Prime Software work under Linux!? References: Message-ID: <9715dd8b-abf7-4b89-b95f-100ed8dfc06f@40g2000prx.googlegroups.com> Hi Dan, I just tried your suggestion with the Crossover Linux. I get the same problems as with wine. To make things run, I borrowed a PC with XP to be able to operate the ?KTA, while I consider the WINE port now as hobby project and I consider to run install a virtual Windows on the Linux Machine. I could resolve an issue where Emain asked for some 32bit alsa- pulse.so files by installing a 32bit library, but now I am running into lots of page faults which have not been displayed before. Then the known messages about stack/heap problems and MFC42.DLL show up. Best reagrds, Wolfgang From norbert.ahrens from charite.de Mon Jan 5 17:07:31 2009 From: norbert.ahrens from charite.de (Dr. Norbert Ahrens) Date: Mon Jan 5 17:51:44 2009 Subject: [Bio-software] RefVal Message-ID: Dear Professor Solberg, I have read very convincing reports about RevVal and would therefore like to ask, if you knew how this application could be available? Thanks for your help! Sincerely, Norbert Ahrens ********************* Dr. med. Norbert Ahrens FA f?r Transfusionsmedizin Charit? ? Universit?tsmedizin Berlin Institut f?r Transfusionsmedizin Augustenburger Platz 1 13353 Berlin Germany From orry.molsoft from gmail.com Mon Jan 12 14:59:26 2009 From: orry.molsoft from gmail.com (Andrew Orry) Date: Mon Jan 12 15:21:38 2009 Subject: [Bio-software] Protein Structure and Drug Design Workshop - MolSoft February 5-6 2009 Message-ID: <496BA11E.80809@molsoft.com> **We still have some places available at out MolSoft ICM Workshop: "Protein Structure and Drug Discovery" February 5th to 6th 2009 La Jolla, CA.** Please see the following invitation to attend MolSoft's (www.molsoft.com) Protein Structure and Drug Design Workshop on February 5th to 6th 2009 in La Jolla, California USA. For more information and a registration form visit www.molsoft.com/training.html. 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 molecular 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/news.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. From vinay.gvteh from gmail.com Sun Jan 25 12:19:10 2009 From: vinay.gvteh from gmail.com (Vinay Kumar) Date: Sun Jan 25 12:35:33 2009 Subject: [Bio-software] Pedro: Free OpenSource Data Entry Tool for Genomics and Proteomics Message-ID: <497c9f14.16048e0a.5002.5bc5@mx.google.com> Hello, Please provide me a tool to do data entry work, and I need to work with the images on the top and entry part in the bottom. Regards, Vinay Kumar From expressionbrowser from gmail.com Wed Jan 28 14:59:53 2009 From: expressionbrowser from gmail.com (expressionbrowser@gmail.com) Date: Wed Jan 28 15:01:14 2009 Subject: [Bio-software] New free online Arabidopsis gene expression search and visualization tool Message-ID: <9a9b0abe-57e5-43ae-9e1f-0c9c7253a870@y1g2000pra.googlegroups.com> Dear colleagues, We newly release Gene Expression Browser for Arabidopsis at http://www.ExpressionBrowser.com. The free online service is very easy to use. Users only take about 10 minutes to view a tutorial video at http://www.ExpressionBrowser.com/video.swf.html and can use it confidently. Gene Expression Browser for Arabidopsis includes the data in 2435 ATH1 chips from 142 independent experiments. The web and software developers remove all concepts of statistics and bioinformatics. Users only need type in keywords to search the results. The web 2.0 interface provides both simple and comprehensive visualization on the complex cross-experimental expression data. Therefore, Gene Expression Browser is a complete, convenient and powerful tool to search and visualize gene expression information. You suggestion and feedback are welcome. GEB develper