[Pipet Devel] updated model

Thomas.Sicheritz at molbio.uu.se Thomas.Sicheritz at molbio.uu.se
Mon Dec 7 03:58:46 EST 1998

J.W. Bizzaro writes:
 > We will only use Python and C for the *core* distribution of TULIP.
 > This is to keep it as simple as possible.  When we say that any language
 > can be added, we mean it is added on top of the core.  We also want to
 > keep the GUI consistent, so we will only endorse the use of GTK/GNOME.
 > I think there are many excellent reasons for using this widget set.
 > There are Python-GTK and Python-GNOME bindings by James Henstridge, so
 > any language that can work with Python can work with GTK/GNOME.

So the other language modules are going to communicate with the core via
e.g. XML ?

 > We also need a list of core TULIP tools that need to be ported to TULIP
 > and/or developed.  Describe some tools for me that *you* think should be
 > in a bioinformatics/modelling package.

I can tell about some tools needed for sequence analysis ...
P=port D=develop

high priority:
* P/D basic sequence format conversions (readseq)
* P sequence alignment (clustalw)
* P/D colored alignment viewer/editor, like seaview
* P setting up and maintain sequence databases like SWISS, EMBL
* P local blast service
* D interface to www blast
* D/P tools to manage blast results
* P Sequence retrieval System (SRS)
* P phylogenetic tools FREE: ( PHYLIP package, Tools from Lyon)

not quite so high priority:
* D simple database engine and interface for ??? LabResults/Sequences ...
* D phylogenetic tools PAY: - integration of PAUP*
* D/P Primer picking
* D/P integration of Sequence assembly programs, like STADEN, Phred&Phrap
* D management of genome sequences

c ya
Sicheritz Ponten Thomas E.  Department of Molecular Biology
blippblopp at linux.nu         BMC, Uppsala University
BMC:  +46 18 4714214        BOX 590 S-751 24 UPPSALA Sweden
Fax   +46 18  557723        http://evolution.bmc.uu.se/~thomas
Molecular Tcl:   http://evolution.bmc.uu.se/~thomas/tcl
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	De Chelonian Mobile ... The Turtle Moves ...

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