HLRnet.com: New teaching software: Biology and anatomy

New software: Biology and anatomy

Microsoft Computational Biology Tools
Computational biology tools from Microsoft Research's Machine Learning and Applied Statistics group: PhyloD (Phylogeny-Based Association Analysis), Epitope Prediction, HLA Assignment, HLA Completion

http://www.codeplex.com/MSCompBio
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER, CHARMM, and MMFF94 force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, secondary structure calculation, molecular editing and docking. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code. In addition, it provides a Python interface with Integrated Development Environment features to allow interactive rapid prototyping.

http://freshmeat.net/projects/ballview/
Bioclipse is a rich-client platform chemistry and biology workbench. It provides access to many open source bioinformatics and chemoinformatics toolkits and has plugins for the Chemistry Development Kit, JChemPaint, Jmol, and BioJava.

http://freshmeat.net/projects/bioclipse
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.

http://freshmeat.net/projects/ball
BALLView is an extensible viewer for bio-molecular structures. It provides all standard models and offers rich functionality for molecular modeling and simulation, including molecular mechanics methods (AMBER and CHARMM force fields), continuum electrostatics methods employing a Finite-Difference Poisson Boltzmann solver, and secondary structure calculation. Since BALLView is based on BALL (the Biochemical ALgorithms Library), it is easily extensible on the level of C++ code and it has an Python interface to allow interactive rapid prototyping.

http://freshmeat.net/projects/ballview/
Wings
Database which manages bird sightings
http://www.versiontracker.com/dyn/moreinfo/win/37667
The Biochemical ALgorithms Library (BALL) is a framework for rapid application development in molecular modeling and structural bioinformatics. BALL provides an extensive set of data structures as well as classes for molecular mechanics, advanced solvation methods, comparison and analysis of protein structures, file import/export, NMR shift prediction, and visualization. Its extensibility results from an object-oriented and generic programming approach.

http://freshmeat.net/projects/ball
BioCoRE is a collaborative work environment for biomedical research, research management, and training. It features easy-to-use tools, among them co-authoring papers and other documents, running applications on supercomputers, sharing molecular visualization over the Internet, notifying project team members of recent project changes by email, chatting, keeping a lab book, and other practical features.

http://freshmeat.net/projects/biocore/
J-Bird is a record keeping system for observations of birds. In the parlance of birders, it is bird listing software. It is oriented toward birding trips. Information recorded includes region, trip date, locality, keywords, notes, species observed, and notes on individual species. It can record sightings, produce trip reports, produce composite lists such as life lists, tally observations by category, and query sightings. Regional checklists can be built, used to record sightings, and be included in trip reports. Sightings can be exported to CSV tables and HTML tables.

http://freshmeat.net/projects/j-bird/
Washington University BLAST is a powerful software package for gene and protein identification, using sensitive, selective, and rapid similarity searches of protein and nucleotide sequence databases.

http://freshmeat.net/projects/wublast
Living Cell 3D Screensaver
Turn your desktop into the eye-piece of a powerful microscope..
http://www.jumbo.com/file/18251.htm
PlantStudio Botanical Illustration Software 1.50
PlantStudio Botanical Illustration Software is a tool for creating pictures of 3D plants. Version 1.50 fixes a bug that occurred when plant files were being imported.
PlantStudio Botanical Illustration Software 1.50, Windows 95/98/NT Shareware:
http://www.softseek.com/files/review?HOGR20980sw
EthoLog 2.1: Behavioral observation tool. Free
EthoLog is a tool for the transcription and timing of behavior observation sessions. The behavioral categories and their keycodes are defined by the user in a text file. EthoLog is designed to deal with two kinds of events: State Events, which have durations, and Instant Events, which have times of occurrence (and are embedded in State Events). The user can add Labels to anyregistered event, which can act as notes or modifiers. The transcription sessions can be paused and resumed. EthoLog generates two text files with a session summary and the full sequential and timing data. These files can be exported to a spreadsheet for further analyses.
Special requirements: Visual Basic 3 runtime file vbrun300.dll.
Freeware. Eduardo B. Ottoni, University of Sco Paulo, Brazil, ebottoni@usp.br, http://www.geocities.com/CapeCanaveral/Lab/2727/ethohome.html.