Software wURLd

Search Bio-wURLd for your favourite URL:

You can contribute your favourite URL to this list:

Contributed URL's

EBI - Documentation, software and services
EBI - The BioCatalog The BioCatalog is a software directory of general interest in molecular biology and genetics. The BioCat is divided in "Domains" and you can also access the catalog that way : DNA , Proteins , Alignments , Genetic , Mapping , Molecular Evolution , Molecular graphics, Database, Servers, Misc. .
EGCG (Extensions to GCG) EGCG is an abbreviation of "Extended GCG". The package began life at EMBL in Heidelberg, Germany as a small collection of programs to support EMBL's research activities, in particular the development of automated DNA sequencing. The programs that resulted were published [1] and released on the new EMBL Network File Server [2] under the name "GCGEMBL". (Submitted by diTommaso@ebi.ac.uk)
The Bioinformatics Resource for Algorithms, Software and Sequences. The BRASS homepage has been designed for the Bioinformatics unit at the University of Manchester School of Biological Sciences. This resource is designed to allow access to different types of Bioinformatics services via the Internet. These include access to Databases, Software and Bulletin Boards.
Melanie Developed on an international level by Denis Hochstrasser and the MELANIE group in Geneva, Switzerland, Melanie II 2-D Analysis Software automates and simplifies the identification, quantitation, and comparison of 2-D samples. Useful for the analysis of many types of samples (IPG gels, silver stained gels, amino-black PVDF membranes, phosphorescence plates, autoradiograms), Melanie II software offers sophisticated analysis for both single and high volume 2-D comparison studies. User-friendly interface, 8, 12, and 16-bit TIFF file import, data management, and worldwide reference capabilities are only some of the features to speed your 2-D analysis (Submitted by roa@diogenes.hcuge.ch)
Swiss-Model Swiss-Model is an Automated Protein Modelling Server running at the GLAXO Institute for Molecular Biology in Geneva, Switzerland (GIMB). The purpose of this server is to make Protein Modelling accessible to all biochemists and molecular biologists World Wide. (Submitted by bairoch@cmu.unige.ch)
IUBio Archive IUBio Archive is an archive of biology data and software. The archive includes items to browse, search and fetch molecular data, software, biology news and documents, as well as links to remote information sources in biology and elsewhere. Molecular biology is the area of concentration, and it is also a home for Drosophila research data. The archive will maintain software for Macintosh, VAX-VMS, Unix, MS-DOS and any other important computer operating systems. (Submitted by Anonymous)
MolScript by Per Kraulis MolScript is a program for creating molecular graphics in the form of PostScript plot files. Possible representations are simple wire models, CPK spheres, ball-and-stick models, text labels and Jane Richardson-type schematic drawings of proteins, based on atomic coordinates in various formats. (Submitted by Anon@uranus.ebi.ac.uk)
RasMol Molecular Visualisation Program (Roger Sayle) RasMol2 is a molecular graphics program intended for the visualisation of proteins, nucleic acids and small molecules. The program is aimed at display, teaching and generation of publication quality images. RasMol runs on Microsoft Windows, Apple Macintosh, UNIX and VMS systems. (Submitted by Anon@uranus.ebi.ac.uk)
GraphPad Software. Intuitive software for science. GraphPad makes simple programs for scientific graphics, curve fitting, and statistics. Programs include GraphPad Prism (graphics and curve fitting for Windows) and GraphPad InStat (truly simple statistics for DOS or Mac). (Submitted by Hmotulsky@graphpad.com)
ALSBYTE Biotechnology Products Molecular biology software for sequence manipulation & analysis, PCR primer selection, vector design, manual sequencing, automated sequencers, MW determination, software for use with hand and desktop scanners for sequence entry, RFLPs and RAPDs, and dot blots. Manufacturers represented are: DNA ProScan, Gene Codes, National Biosciences, Hitachi, with more to come. (Submitted by Betsy Alberty email: alsbyte1@well.com)
NAOMI is developed by Simon M. Brocklehurst. NAOMI is aimed at researchers who make use of atomic-level, three-dimensional structures of proteinsin their work. NAOMI provides interfaces to the graphics programs MOLSCRIPT, INSIGHT II and QUANTA, , as well as its own graphical output, to allow efficient visualizations of the results of calculations and analyses. (Submitted by Anon@uranus.ebi.ac.uk)
ProFit - Protein least-squares fitting A flexible interactive program for least-squares fitting.Allows specification of zones and atoms for fitting,calculation of RMS over other zones, RMS by residue, etc. (Submitted by Andrew C.R. Martin, martin@biochem.ucl.ac.uk)
QTree - Molecular rendering QTree generates CPK, ball and stick and worms imagesusing the quad-tree algorithm. Images may be displayedusing the ImageMagick software. (Submitted by Andrew C.R. Martin, martin@biochem.ucl.ac.uk)
BiopLib - C library for protein manipulation An extensive library of C routines for the manipulation of protein structure. Also included is a library of routines for more general C programming. (Submitted by Andrew C.R. Martin, martin@biochem.ucl.ac.uk)
WWW2GCG User Manual Written by Marc Colet (mcolet@ulb.ac.be), at the Belgian EMBnet Node, WWW2GCG is an set of programs and scripts created with the hope to provide users with a friendly interface to the GCG software. If the EGCG 8.0 programs are installed at your site, they will also be interfaced! (Submitted by ditommaso@ebi.ac.uk)
VMD VMD is a molecular graphics program for the interactive visualization of large biomolecular systems. It can display multiple molecules in many different styles simultaneously, including CPK, ribbon, tube, and molecular or solvent accessible surface. It is designed for researchers using medium to high end SGIs. Full documentation, source code, and IRIX 5.x binaries are available at no cost. is freely (Submitted by vmd@ks.uiuc.edu)
namd namd is a free parallel molecular dynamics program developed for distributed memory parallel machines, such as workstation clusters. It is designed to be fast and easy to modify so new features may be added as needed. Current features include fast multipole calculation for complete electrostatics calculation, CHARMm-19 and -22 force fields, and Langevin dynamics. Complete C++ source code and user's and programmer's manual's are available at no charge. (Submitted by namd@ks.uiuc.edu)
Signal Scan SIGNAL SCAN finds homologies of published signal sequences in your sequence, most of these transcriptional elements. (Submitted by Eric Ness eness@biosci.cbs.umn.edu)
Promoter Scan Promoter Scan is designed to find putative eukaryotic Pol II promoter sequences in primary sequence data (Submitted by Eric Ness eness@biosci.cbs.umn.edu)
MEMSAT - MEMbrane protein Structure And Topology. MEMSAT is a program which predicts the secondary structure and topology of all-helix integral membrane proteins based on the recognition of topological models. The method employs a set of statistical tables (log likelihood ratios) compiled from well- characterized membrane protein data, and a novel dynamic programming algorithm to recognize membrane topology models by expectation maximization. The statistical tables show definite biases towards certain amino acid species on the inside, middle and outside of a cellular membrane. The method is described in the following reference: Jones, D.T., Taylor, W.R. and Thornton, J. M. (1994) Biochemistry. 33:3038-3049. (Submitted by ditommaso@ebi.ac.uk)
BIO Online Store Online store for commercial Life Sciences related software. Biotech, molecular modeling, qsar, medicine, productivity, education, etc. Main URL is www.bio.com. Store requires secure Netscape, non secure version to be added for other browsers. (Submitted by sunger@bio.com)
CTI Biology Resource Directory A searchable and browsable database of software and other resources of use to teachers of biological subjects at university level. (Submitted by Paul Gould (P.W.Gould@liverpool.ac.uk))
BioSoftware Marketing Over 400 life sciences software titles on sale (in BIO Online Store at www.bio.com). Marketing and consulting capabilities described. (Submitted by stefan unger sunger@a.crl.com)
Plasmid Processor software Plasmid Processor is a simple tool for plasmid presentation for scientific and educational purposes. It features both circular and linear DNA, user defined restriction sites, genes and multiple cloning site. In addition you can manipulate plasmid by inserting and deleting fragments. Created drawings can be copied to clipboard or saved to disk for later use. Printing from withing program is also supported. (Submitted by anon)
Molecular Modeling programs Useful list of molecular modeling programs... Rasmol, Molmol, Entrez MolMol etc. (Submitted by Anon@croma.ebi.ac.uk)
PESTFIND The PEST search utitlity identifies possible PEST regions in a submitted probe using the Molecular fraction of the P, E, S and T components, and the hydrophobicity index of the region. (Submitted by Anon@croma.ebi.ac.uk)
A list of linkage analysis software A comprehensive list of computer software on genetic linkage analysis and genetic mapping construction (Submitted by anon)
WWWtacg For those of you who have been requesting a Web-available resource for Restriction Enzyme analysis and mapping, here are the URLs for the WWW interface to 'tacg', my freely available, command-line restriction enzyme analysis tool for unixy systems: (Submitted by mangalam@uci.edu)
Molecular Linux Molecular Biology related programs for Linux (Submitted by thomas@evolution.bmc.uu.se)
SeqSearch multi-user/multi project SeqSearch v1.0 for Windows, DNA analysis package (Submitted by Niels Groot marker@xs4all.nl )
Chromas 1.3 Chromas is a Windows application which displays and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF and Li-Cor sequencers can create. (Submitted by Conor McCarthy c.mccarthy@sct.gu.edu.au)
Protein Colourer II Tool for colouring proteins (Submitted by tommaso@ebi.ac.uk)
AnTheProt: ANTHEPROT (ANalyze THE PROTeins) is a package to make protein sequence analysis such as alignment, secondary structure predictions , sites & function detection, physico-chemical profiles, homology search and 3D display of protein structures. (Submitted by Rab C. Nesbit)
W2H - WWW interface to GCG I have a pleasure to announce a new release (1.3) of the "W2H - WWW interface to GCG" (Submitted by Martin Senger )
DYNAFIT DynaFit executable files (PowerMac, DOSbox under Win31,Win95,WinNT) (Submitted by Petr Kuzmic pkuzmic@biokin.com)

Bio-wURLd is a searchable, user-maintained collection of URL's related to bioinformatics, biochemistry, and molecular biology.