[Pipet Devel] links

[J.W. Bizzaro]

Konrad and Jay,

I did some searching for applications that might be helpful for us to
take a look at.  Below are links to sites about algorithms that may be
incorporated into TULIP and some projects that might parallel TULIP to
some extent:

The following four sites have GNU GPL licensed tools.  If the core
distribution of TULIP is to be all GPL, we need to look for tools that
are also GPL.

              Software from the Eddy Lab
              http://www.genetics.wustl.edu/eddy/software/

              The Sanger Centre : Dynamite 
              http://www.sanger.ac.uk/Software/Dynamite/

              SCRate 
              http://www.mrc-lmb.cam.ac.uk:80/genomes/jong/SC_rate.html

              The Sanger Centre : Wise2 
              http://www.sanger.ac.uk/Software/Wise2/

The following are tools that are not GPL, but they are free, and the
source code is available.  So, the authors may be willing to make it
GPL.  If not, we can put them in a separate distribution.

              FETCH 
              http://ind5.mrc-lmb.cam.ac.uk/fetch_home.html

              The Babel Home Page 
              http://mercury.aichem.arizona.edu/babel.html

              Cn3D Home Page 
              http://www.ncbi.nlm.nih.gov/Structure/cn3d.html

              Democritos Home Page 
              http://www.seqnet.dl.ac.uk/CBMT/democ/HOME.html

              The Sanger Centre : Dotter [not GPL???]
              http://www.sanger.ac.uk/Software/Dotter/

              NJplot 
              http://pbil.univ-lyon1.fr/software/njplot.html

              tacg Version 2 - Documentation 
              http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.main.html

The following are some projects that provide rather large packages for
DNA and protein analyses.  They may not be directly competing with TULIP,
but they may give us some ideas.

              FASTA 
              ftp://ftp.virginia.edu/pub/fasta/

              Geanfammer home page : genome analysis and protein family maker 
              http://www.mrc-lmb.cam.ac.uk/genomes/geanfammer.html

              SEALS Home Page 
              http://www.ncbi.nlm.nih.gov/Walker/SEALS/index.html

              SeqPUP
              http://iubio.bio.indiana.edu/IUBio-Software+Data/molbio/seqpup/

The following are some Java-based packages, tools, and links to tools.
Many bioinformaticists believe Java is _the_ language for the job, but
others (as myself) tend to disagree.  The advantages TULIP has over Java
are that the compute-intensive stuff can be compiled, making TULIP much
faster, and TULIP will be language independent (see next e-mail).

              Base4 Java Bioinformatics Links 
              http://telomere.base4.com/html/java_list.html

              Javascript, Java and CORBA 
              http://bioinformatics.weizmann.ac.il/comp/java_info.html

              Java-based Molecular Biology Work Bench 
              http://www.embl-heidelberg.de/~toldo/JaMBW.html

              Neomorphic Software, Inc.'s Java Demos 
              http://www.neomorphic.com/demo/

              bioWidget Consortium 
              http://www.biowidgets.org/

              BioObjects: CORBA in Bioinformatics 
              http://sunny.ebi.ac.uk/BioObjects/

              CBIL bioWidgets for Java(tm) 
              http://www.cbil.upenn.edu/bioWidgets/

              AppLab Homepage 
              http://industry.ebi.ac.uk/applab/

So far, I have found _no_large_bioinformatics_package_with_GNU_GPL_code_!


Jeff
-- 
J.W. Bizzaro                  Phone: 617-552-3905
Boston College                mailto:bizzaro at bc.edu
Department of Chemistry       http://www.uml.edu/Dept/Chem/Bizzaro/
--