Catalogue of Molecular Biology Programs Release 6.1 23 Jul 1999 All thanks are in the file biocatal.thanks. ===================================================================== AC BC00117 NAME DNA-GUI DOMAIN Image analysis DESCRIPTION software program for assisting in the DESCRIPTION quantitative analysis of 1D-electrophoretic- DESCRIPTION gel images. AUTHOR Heather A. Drury et. al. RA Drury H.A., Clark K.W., Hermes R.E., Feser J.M., Thomas L.J., RA Donis-Keller H.; RT "A Graphical User Interface for Quantitative RT Imaging and Analysis of Electrophoretic Gels RT and Autoradiograms"; RL Biotechniques 12(6):892-901(1992). ADDRESS Institute for Biomedical Computing, ADDRESS Biomedical Computer Laboratory, Washington University ADDRESS 700 S. Euclid Ave., St. Louis MO 63110 USA CONTACT kwc@ibc.wustl.edu SITE ftp anonymous ftp.bio.indiana.edu SITE Directory /molbio/unix SITE-CONTACT D Gilbert : gilbertd@cricket.bio.indiana.edu SITE WWW Server at URL http://ibc.wustl.edu/bcl/dnagui/dnagui_home.html OS UNIX workstations using the X Window system LANGUAGE C VOLUME - AC BC00118 NAME IMAGE DOMAIN Image analysis DESCRIPTION A system for processing restriction digest DESCRIPTION fingerprint gels has been developed.Image 3 is the latest DESCRIPTION version, and can process gel images from a wide variety of DESCRIPTION sources, including fluorescent ABI gel images. The package DESCRIPTION includes automated tools and editing tools for band DESCRIPTION calling, lane tracking and normalizing band data from DESCRIPTION standards. The system is designed to work closely with DESCRIPTION FPC. AUTHOR Darren Platt, Friedemann Wobus RA Sulston J., Mallett F., Staden R., Durbin R., Horsnell T., RA Coulson A.; RT "Software for genome mapping by fingerprinting techniques."; RL Comput. Appl. Biosci. 4(1):125-132(1988). ADDRESS Sanger Centre, Hinxton Hall, Hinxton, Cambridge, CB10 1SA, UK CONTACT image@sanger.ac.uk SITE http://www.sanger.ac.uk/fingerprinting/imageprocessing SITE-CONTACT - OS irix4, sunos 4.1.X, solaris 2.x, OSF, Linux LANGUAGE ANSI-C/C++ VOLUME - REQUIRES X11 AC BC00119 NAME LABOIMAGE DOMAIN Image analysis DESCRIPTION Labo Image is a window based software for image processing and analysis. DESCRIPTION It contains a comprehensive set of operators as well as general utilities. DESCRIPTION It is designed to be open-ended; new modules can easily be added. The software, DESCRIPTION written in C, is now based on X11 / OSF Motif. The current version has been DESCRIPTION developped and tested on a Sun SPARC station, with X11r4 and Motif 1.1. DESCRIPTION LaboImage has been extensively used by students as well as researchers from DESCRIPTION various domains: computer science (image analysis), medicine, biology, physics. DESCRIPTION It is distributed free of charge (source code). AUTHOR A. Jacot-Descombes, M. Rupp, T. Pun RA Jacot-Descombes A., Rupp M., Pun T.; RT "LaboImage: A portable window-based environment for research in RT image processing and analysis."; RL SPIE Symposium on Electronic Imaging Science and Technology, Image RL Processing: Implementation and Systems, San Jose, California, USA, RL Feb. 9-14, 1992. ADDRESS Thierry Pun,LaboImage Computing Science Center, ADDRESS University of Geneva, 24, rue du General-Dufour ADDRESS CH - 1211 Geneva 4, SWITZERLAND ADDRESS tel.: +(41 22) 705 76 27 (T. Pun), 705 76 30 (A. Jacot-Descombes) ADDRESS fax: +(41 22) 320 29 27 CONTACT pun@uni2a.unige.ch SITE ftp anonymous cui.unige.ch SITE Directory /PUBLIC/vision/software SITE-CONTACT - OS SunOS 4.1.x, Solaris 2.x LANGUAGE C VOLUME ~ 11 Mb REQUIRES X11/ OSF motif AC BC00493 NAME MATRIX DOMAIN Image analysis DESCRIPTION QuantaVision Canada is happy to announce the DESCRIPTION commercial release of MATRIX: a Gel Imaging software DESCRIPTION package designed to locate and quantitate DNA/RNA/protein DESCRIPTION bands from images derived from a variety of sources, DESCRIPTION including: protein gels, PCR/DNA gels, RFLP gels, DESCRIPTION Northerns, Southerns, and Westerns blots. Over a year in DESCRIPTION development and use, the program was designed to provide DESCRIPTION research scientists with a powerful and easy to use DESCRIPTION Windows-based tool that exceeds the features of present-day DESCRIPTION DOS and Windows-based programs. DESCRIPTION Unlike most image analysis software, MATRIX DESCRIPTION was designed to accept images from most CCD-based image DESCRIPTION capturing systems and scanners, making it compatible with DESCRIPTION virtually all existing systems. In addition, MATRIXs DESCRIPTION comprehensive help file and tutorials make learning so easy DESCRIPTION and intuitive, most users master the softwares capabilities DESCRIPTION within a single hour. AUTHOR QuantaVision Canada RT - ADDRESS - CONTACT biocan@vir.com SITE WWW Server at URL http://www.vir.com/~biocan/ OS Win 3.x/Win 95 LANGUAGE - VOLUME - REQUIRES 486/Pentium with 8MB of RAM minimum AC BC00519 NAME ONIX DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN Image analysis DESCRIPTION PC-based program for Windows, ONIX, allows DESCRIPTION users to examine proteins with known 3D structure from PDB. DESCRIPTION This program was designed for structure investigation of DESCRIPTION ligand binding site in proteins. The last one is a DESCRIPTION combination of certain fragments of protein sequence. Its DESCRIPTION examination requires active participation both of human and DESCRIPTION computer in the process of investigation. ONIX is an DESCRIPTION interactive software with high-performance interface, fast DESCRIPTION 3D molecular graphics and analysis of water-accessible DESCRIPTION surface. This program was designed based on protein DESCRIPTION structure hierarchy. Analysis of molecular surface makes DESCRIPTION possibly to find all elements of ligand binding site. AUTHOR A.S.Ivanov, A.B.Rumjantsev, V.S.Skvortsov, A.I.Archakov RA Ivanov A.S., Rumiantsev A.B., Skvortsov V.S., Archakov A.I.; RT "ONIX: an interactive PC program for the examination RT of protein 3D structure from PDB."; RL Comput. Appl. Biosci. 13:111-113(1997). ADDRESS Prof. Alexis S. Ivanov ADDRESS Institute of Biomedical Chemistry, ADDRESS Pogodinskaya str. 10, ADDRESS Moscow, 119832, Russia. CONTACT ivanov@ibmh.msk.su SITE ftp anonymous org.chem.msu.su SITE Directory pub/software/Onix/ SITE-CONTACT - OS Windows 3.1 or higher LANGUAGE - VOLUME 1.5 Mb REQUIRES PC 386/387 or higher, SVGA 512 kb, Windows 3.1 or higher, REQUIRES graphics mode 640 x 480 x 256 colors. COMMENTS For 3D visualization put marks in the lists and COMMENTS then press key F5 (read Manual in MS WinWord file). AC BC00586 NAME Active Shape Model Toolkit DOMAIN Image analysis DESCRIPTION The Active Shape Model (ASM) Toolkit is designed to tackle DESCRIPTION a wide range of 2D visual inspection tasks including DESCRIPTION detection, recognition, measurement, classification, and DESCRIPTION tracking. The ASM Toolkit provides leading edge image DESCRIPTION interpretation software for the description and recognition DESCRIPTION of objects whose shape can vary. DESCRIPTION DESCRIPTION The benefits of the ASM Toolkit are that visual models DESCRIPTION (Active Shape Models) can be built that describe the shape DESCRIPTION of many objects. ASM technology has been used for modelling DESCRIPTION and locating bones in medical images; inspecting components DESCRIPTION in car brake assemblies; and modelling and recognising faces. DESCRIPTION The ASM Toolkit is sold as an add-on product for use with DESCRIPTION MATLAB 5.2, and is available for Windows 95/NT, and Solaris 2.5. AUTHOR David Butcher, Tim Cootes, Kevin Walker, Gareth Edwards RA Cootes T.F., Taylor C.J.T., Cooper D.H., Graham J.; RT "The Use of Active Shape Models for Locating Structures RT in Medical Images"; RL Image and Vision Computing. 12(6), July 1994. ADDRESS Visual Automation Ltd ADDRESS Stopford Building ADDRESS Oxford Road ADDRESS Manchester ADDRESS M13 9PT ADDRESS UK CONTACT d.butcher@vuman.co.uk SITE - SITE-CONTACT - OS Windows 95/NT, Solaris 2.5 LANGUAGE C++ VOLUME 1.0 REQUIRES MATLAB 5.2 COMMENTS The Active Shape Model techniques originated in the Wolfson COMMENTS Image Analysis Unit (WIAU), a world renowned research group COMMENTS situated in the Medical School of the University of COMMENTS Manchester (UK). Visual Automation Ltd are the technology COMMENTS transfer arm of the WIAU. COMMENTS COMMENTS The generic techniques have been widely applied to numerous COMMENTS image interpretation problems in medical, industrial, and COMMENTS scientific fields. The ASM techniques are most appropriate COMMENTS for modelling objects that have a natural variation, such as COMMENTS hands, faces, medical organs and bones, leaves, insects. AC BC00594 NAME Protein Adviser for Windows DOMAIN Sequence format conversion tools DOMAIN Sequence display DOMAIN Protein sequence analysis DOMAIN Protein structure analysis DOMAIN Molecular modelling and graphics DOMAIN General tools DOMAIN Chemistry DOMAIN Image analysis DOMAIN Comparative analysis DOMAIN Protein 3D visualisation, editing and analysis (QSAR) DESCRIPTION FQS Protein Adviser displays and analyses 3D structures of DESCRIPTION biological molecules such as proteins or nucleic acids. DESCRIPTION Protein Adviser is a powerful tool for visual and numerical DESCRIPTION investigation of protein molecules and their 3D structures. DESCRIPTION The new implementation for Windows 95/98 and NT uses the DESCRIPTION innovative Microsoft technology for rendering molecular DESCRIPTION graphics known as Direct3D. Using Direct 3D technology FQS DESCRIPTION created the fastest biomolecular viewer available on PC DESCRIPTION platform. DESCRIPTION Versatile features to support protein analysis: DESCRIPTION - sequence based 3D analysis DESCRIPTION - Three level selections: atoms, residues, molecules DESCRIPTION - Display/Hide hydrogen's DESCRIPTION - Display/Hide side chain DESCRIPTION - Hydrogen generation DESCRIPTION - Measure atom-atom distances DESCRIPTION - Compare 3D structures DESCRIPTION - Compare aminoacid sequences DESCRIPTION - Analyze Ramachandran plots DESCRIPTION - Mutate and change side chain conformations DESCRIPTION - Build proteins, change torsional angles DESCRIPTION - Copy and paste molecules between the windows DESCRIPTION - Rotate and move selected molecules DESCRIPTION Windows specific features DESCRIPTION Protein Adviser can open as many documents DESCRIPTION as you wish and analyse them within one program session, DESCRIPTION Protein Adviser implements full ActiveX/OLE2 functionality. DESCRIPTION Its objects (molecules) may be placed on your WEB page and DESCRIPTION visualized by your colleagues everywhere through the DESCRIPTION internet. DESCRIPTION Plotting hydrophobicity and other properties DESCRIPTION Protein Adviser for Windows can plot DESCRIPTION different named properties. The program comes with 3 DESCRIPTION different scales of hydrophobicty, including Kyte&Doolittle DESCRIPTION scale. The program includes also 6 other predefined QSAR DESCRIPTION methods. DESCRIPTION Plotting Ramachandran diagrams DESCRIPTION Ramachandran plots show two-dimensional DESCRIPTION histograms of the values of conformational angles phi and DESCRIPTION psi. These histograms are superimposed on the areas of DESCRIPTION allowed and forbidden conformational angles pair values. DESCRIPTION Aminoacids DESCRIPTION Protein Adviser displays sequences of DESCRIPTION aminoacids as 3-letter codes, 1-letter codes or secondary DESCRIPTION structure symbols DESCRIPTION Protein's 3D structure comparison DESCRIPTION Protein Adviser for Windows allows for DESCRIPTION protein structure comparison command. The program DESCRIPTION superimposes the protein's 3D structures based on C(alpha) DESCRIPTION atoms coordinates and RMSD analysis. AUTHOR FQS Ltd. (Fujitsu Kyushu System Engineering Ltd.) RT - ADDRESS FQS Poland Sp. z o.o. ADDRESS Palac Pugetow ADDRESS ul. Starowislna 13-15 ADDRESS 31-038 Krakow ADDRESS Poland ADDRESS Tel. (+48 12) 4294345 ADDRESS Fax. (+48 12) 4296124 CONTACT info@fqspl.com.pl SITE WWW Server at URL http://www.fqspl.com.pl/protein OS Windows 95/98/NT, Macintosh LANGUAGE English, Japanese VOLUME 10 MB REQUIRES PC Pentium 166, 16MB RAM, Microsoft DirectX COMMENTS Commercial software. COMMENTS Price: COMMENTS 800 USD - commercial license & COMMENTS 400 USD - academic licence AC BC00603 NAME Cross Checker DOMAIN Image analysis DESCRIPTION Interpretation assistance software for RAPD & AFLP gel images. DESCRIPTION Results can be exported to phylogenetic or genetic DESCRIPTION linkage software. AUTHOR J.B. Buntjer RT - ADDRESS Laboratory of Plant Breeding ADDRESS Wageningen UR ADDRESS P.O. Box 386 ADDRESS 6700 AJ Wageningen ADDRESS The Netherlands CONTACT jaap.buntjer@users.pv.wau.nl SITE WWW Server at URL http://www.spg.wau.nl/pv/pub/CrossCheck/index.html OS Windows95 LANGUAGE - VOLUME - REQUIRES -