PerlMol — Perl Modules for Molecular Chemistry

Posted on April 23, 2004 by Dan Gezelter

PerlMol is a collection of Perl modules for chemoinformatics and computational chemistry with the philosophy that "simple things should be simple". It should be possible to write one-liners that use this toolkit to do meaningful "molecular munging".
Find PerlMol — Perl Modules for Molecular Chemistry at: http://www.perlmol.org

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Required Reading

Posted on April 3, 2004 by Dan Gezelter

We added a Required Reading section today with links to very important essays and debates.

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Open Source / Open Science

Posted on April 3, 2004 by Dan Gezelter

Coverage of the Event from Dr. Dobbs Journal
Find Open Source / Open Science at: http://www.ddj.com/documents/s=891/ddj9975q/9975q.htm

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Open Source / Open Science

Posted on April 3, 2004 by Dan Gezelter

Coverage of the event from the Chronicle of Higher Education
Find Open Source / Open Science at: http://www.chronicle.com/free/v46/i11/11a05101.htm

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Catalyzing Open Source development in science

Posted on April 3, 2004 by Dan Gezelter

Dan Gezelter’s talk at the 1999 BNL open source/open science conference.
Find Catalyzing Open Source development in science at: http://www.openscience.org/talks/bnl

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Homesteading the Noosphere by Eric Raymond

Posted on April 3, 2004 by Dan Gezelter

An excellent followup to "The Cathedral and the Bazaar". The hacker ethic as a gift economy.
Find Homesteading the Noosphere by Eric Raymond at: http://www.catb.org/~esr/writings/cathedral-bazaar/homesteading/

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Nature Magazine’s Open Access Debate

Posted on April 3, 2004 by Dan Gezelter

The Internet is profoundly changing how scientists work and publish. New business models are being tested by publishers, including open access, in which the author pays and content is free to the user. This ongoing web focus will explore current trends and future possibilities. Each week, the website will publish specially commissioned insights and analysis from leading scientists, librarians, publishers and other stakeholders, as well as key links, and articles from our archive.
Find Nature Magazine’s Open Access Debate at: http://www.nature.com/nature/focus/accessdebate/

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Genie

Posted on March 25, 2004 by Dan Gezelter

A program for the inference of demographic history from molecular phylogenies. It is primarily designed for the analysis of phylogenies reconstructed from highly variable viral gene sequences, but can be applied to other types of sequence data that contains a significant amount of phylogenetic information.
Find Genie at: http://evolve.zoo.ox.ac.uk/Evolve/Genie.html

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Phylogen

Posted on March 25, 2004 by Dan Gezelter

Phylogen implements some straight-forward birth-death models for simulating phylogenies. It is intended to be fast and flexible and can simulate very large trees (depending on memory and speed of computer). It will then optionally reconstruct trees only containing extant lineages or produce trees containing a random sample of lineages. Trees can be written to a file for analysis in other packages. It will also draw lineages-through-time-plots.
Find Phylogen at: http://tree.bio.ed.ac.uk/software/phylogen/

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Evolution and Population Genetics Day!

Posted on March 25, 2004 by Dan Gezelter

Thursday is Evolution and Population Genetics day. Two new links, both from the Oxford Evolutionary Biology Group. Genie infers demographic history from molecular phylogenies, and Phyl-O-Gen uses some straight-forward birth-death models to simulate phylogenies.

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