Date: Thu, 7 Jun 2001 12:19:03 +0200 From: Johann Visagie <johann@egenetics.com> To: Will Andrews <will@physics.purdue.edu> Cc: FreeBSD Ports <ports@FreeBSD.org>, portmgr@casimir.physics.purdue.edu, bio@freebsd.net Subject: Re: biology/ && misc/ -> science/ Message-ID: <20010607121903.K30512@fling.sanbi.ac.za> In-Reply-To: <20010515133250.Q11113@casimir.physics.purdue.edu>; from will@physics.purdue.edu on Tue, May 15, 2001 at 01:32:50PM -0500 References: <20010515133250.Q11113@casimir.physics.purdue.edu>
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Will Andrews on 2001-05-15 (Tue) at 13:32:50 -0500: > > I would like to move all non-biology-related science stuff from > biology/* and misc/* to science/. Basically everything that's physical > science related that doesn't already have an appropriate category (e.g. > biology or math). Sorry for chiming in at this late stage - I'm only catching up on the ports list now... > The following repocopies are hence requested (sorry for long lines): The following packages are purely of use to bioinformaticists and computational biologists. If we are to retain a "biology" category, I would suggest that they stay there (along with other closely related packages such as p5-bioperl and py-biopython): > biology/emboss --> science/emboss: genetic sequence analysis > biology/fasta --> science/fasta: A collection of programs for searching DNA and protein databases > biology/fasta3 --> science/fasta3 > biology/fastdnaml --> science/fastdnaml: The faster variant of DNAML, makes phylogenetic trees using maximum likelihood > biology/genpak --> science/genpak: small utilities to manipulate DNA sequences > biology/p5-AcePerl --> science/p5-AcePerl: Perl5 interface to the ACEDB genome database system > biology/paml --> science/paml: Phylogenetic Analysis by Maximum Likelihood (PAML) > biology/phylip --> science/phylip: A Phylogeny Inference Package > biology/seaview --> science/seaview: Multiple DNA sequence alignment editor > biology/sim4 --> science/sim4: An algorithm for aligning expressed DNA with genomic sequences (I'm the maintainer of some of the packages listed above, and others are maintained by people on the unofficial freebsd-bio mailing list, so I have a fair idea of how they're used. :-) Many of the molecular visualisation packages are highly adapted to organic chemistry, and would therefore again only be of use to biochemists. It may make sense to keep them in "biology" as well. This isn't my field, so I can't say with authority which of the following packages fall into this category. I would suggest contacting (where possible) the maintainers...? (If necessary, I can check with some of the biochemists who work with me as well...) > biology/babel --> science/babel: molecular file format conversion > biology/deft --> science/deft: Density functional molecular orbital calculation > biology/gaussian98 --> science/gaussian98: An ab-initio molecular orbital calculation program > biology/kinemage --> science/kinemage: molecular visualization program > biology/molden --> science/molden: Display molecular orbitals and electron densities in 2D and 3D > biology/mopac --> science/mopac: Semi-empirical molecular orbital calculation > biology/platon --> science/platon: Tool for viewing molecular/crystallographic structures > biology/povchem --> science/povchem: Simple yet powerful tool to generate POV from a PDB file > biology/psi88 --> science/psi88: Plotting wavefunctions (molecular orbitals) in 3D > biology/rasmol --> science/rasmol: Fast Molecular Visualization Program > biology/tinker --> science/tinker: A general purpose molecular modelling package The follwing ones sound (to me) more like pure chemistry packages which may make more sense under "science". Again, I may be mistaken in some cases: > biology/chemeq --> science/chemeq: chemical equation to LaTeX > biology/gperiodic --> science/gperiodic: Displays a periodic table of the elements > biology/xdrawchem --> science/xdrawchem: Chemical drawing program > biology/xmolwt --> science/xmolwt: Calculate formula weight and percent of each element for a given formula > misc/xgas --> science/xgas: chemical process I suppose one will always run into problems and differences of opinion when you start classifying things like these. For instance, where do you classify packages which are of exclusive use to biochemists? After all, biochemistry sits somewhere between biology and chemistry (though traditionally, I believe academic biochemists probably feel they have more in common with biologists than with anorganic chemists). -- Johann To Unsubscribe: send mail to majordomo@FreeBSD.org with "unsubscribe freebsd-ports" in the body of the message
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