BioPHP: PHP for Biocomputing

Last updated: May 11, 2003

Project Status top

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TASK / ACTIVITY ASSIGNED TO STATUS
"Parser" class to replace SeqDB class Nico S, Sean C Almost finished
Interfaces with Clustal seq alignment app Nico S, Sean C Almost finished
eFetch / eUtils for querying NCBI databases Sean C Ongoing
Enzyme class Serge G Almost finished
Compound class Serge G Almost finished
Reaction class Serge G Ongoing
Biological Pathway::Enzyme-Enzyme Relations class Serge G Ongoing
Genome class Serge G Just started
Biomedical Literature::Journal class Serge G Just started
Motif class Serge G Just started
Gene class Serge G Just started
Levenshtein Distance method Frankie A Finished
Scoring Matrices (equal length strings) Frankie A Finished
Improving efficiency of existing code Rogelio N Ongoing
Testing various modules Joel R Finished

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Project History top

  April 22 - present

  1. Developing a master framework/blueprint/roadmap for (includes data modeling, etc.)
  2. Various modules to interface with Clustal (a multiple sequence alignment program) and other apps.
  3. Developing my own alignment algorithm which uses recursion.
  4. Writing module that exports GenBank sequences to a MySQL database.
  5. Developing and searching for tools that enhance presentation of sequence and related data.

  April 12-22, 2003. Posted some simple scripts I wrote. The primary aim is to demonstrate the use of
  classes and methods like translate(), charge(), chemgrp(), and the possibilities of interfacing with a relational
  database like MySQL.

  April 5-11, 2003. Posted some bioinformatics PERL scripts I've written. Added/updated the LINKS section.
  Added an iFAQ page. Fixed some broken links. The new site at genephp.sourceforge.net also went live this week.

  April 4, 2003. Bug alert!

   In the SeqDB() constructor method, when the database format is "GENBANK", I used ID (which is the LOCUS NAME)
   instead of PRIMARY ACCESSION as primary key in the *.IDX files. This will be corrected in 1.1.

   April 1, 2003. Updated seq.inc (added trunc() method, moved is_mirror(), is_palindrome(), find_mirror() inside class Seq),
   and the Technical Documentation (both HTML and Word versions). There may still be some discrepancies between the
   documentation and the actual code. Please bear with us. Thank you.

   March 28, 2003. Updated code in seqdb.inc to incorporate support for the SwissProt format.

   March 25, 2003. Posted source code for the SeqAlign Class (seqalign.inc) and an updated Tech. Doc.

   March 19, 2003. Posted the How To and the Source Code.

   March 15, 2003. Posted the Technical Documentation (MS Word format).

   Feb 28, 2003. I start work on BioPHP (then called GenePHP), armed with only a biochemistry
    book and a copy of Bioperl on my machine.

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Join Us! top

You can join or help us in many ways:

  1) You can join our mailing-list the moment it is setup (before the 1st of June?).
  2) You can write and submit BioPHP code. We'll be identifying modules-that-need-to-be-written pretty soon.
  3) You can QA (test code) for us. Bug-hunting is an art in itself.
  4) You can help us with website development and promotion.
  5) You can be a bioscience expert -- someone we can consult from time to time.
  6) You can join us in brainstorming ideas on how to improve BioPHP, etc.
  7) You can submit useful bioinformatics links to us.
  8) Last but not the least, you can provide good ole moral support, so we'll be inspired to go on and on and...

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Copyright © 2003 by Sergio Gregorio, Jr.
All rights reserved.