More Projects at The Open Lab - Bioinformatics.org

J.W. Bizzaro • February 8, 2001

More Projects at The Open Lab

Since September, eight more projects have chosen to use The Open Lab project management system. These projects can be accessed through our website. They are briefly described here in alphabetical order:

(1) BioLib FORTRAN Library (by Francis Meng-Juei Hsieh):

``In order to avoid re-inventing the wheel, a collection fortran codes may be useful for your scientific program.''

(2) DNACGR (by Indraneel Majumdar):

``Program to visualise patterns in DNA and RNA by using Chaos Game Representation''

(3) E-CELL (by Kouichi Takahashi et al):

``E-CELL Simulation Environment (E-CELL SE) is a software package for cellular and biochemical modeling and simulation. E-CELL attempts to provide a framework not only for analyzing metabolism, but also for higher-order cellular phenomena such as gene regulation networks, DNA replication, and other occurrences in the cell cycle.''

E-CELL has three concurrently developed versions hosted at The Open Lab: E-CELLs 1-3.

(4) FreeMOL (by Warren L. DeLano):

``FreeMOL is an assembly of free and open source programs forming a framework for computational chemistry, informatics, structural biology and graphics. FreeMOL will be a credible alternative to high-priced commercial packages.''

(5) GeneGnome (by Deanne Taylor):

``GeneGnome will allow users to build, in the GUI, nodular models of linked cellular enzyme networks in a GNOME environment with the goal of using the underlying calculational engine linked to the GUI to help make testable predictions in real cells.''

(6) Genpak (by January Weiner III):

``Genpak is a set of simple tools for manipulation of nucleic and protein sequences, written in ANSI C. The programs are supposed to be small, efective, use the Unix pipe/redirect and have a GUI via WWW/CGI.''

(7) Open LIMS (by Byron Ellis):

``An open source laboratory information system designed aimed at small labs who want security and data exchange in an open system based on public protocols.''

(8) SMS (by Paul Stothard):

``The Sequence Manipulation Suite is a collection of web-based programs for analyzing and formatting DNA and protein sequences.''

The SMS algorithms are actually implemented in JavaScript. Very cool.

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