[Biojava-l] Newbie questions

[Matthew Pocock]

Hi Michael,

Michael Giddings wrote:

> Hello all,
> I have been looking at BioJava to see if it would be of benefit for some of
> our work here (and whether we could contribute).  I have some newbie type
> questions:

Cool.

> 2. Why doesn't SimpleSequence or SimpleSymbolList have a constructor which
> takes a string as input to initialize the sequence?  Was this intentional
> (i.e. am I missing something), or just a feature nobody has needed yet?
>

The symbol objects are much more semanticaly rich than chars can ever be.
Because of that, we need a layer of insulation between strings of DNA chars and
SymbolList objects representing DNA. This is achieved using SymbolParser
objects. If you just want a quick-and-dirty way to make a DNA sequence from a
string, try:

SymbolList sl = DNATools.createDNA(sequenceString);

Thomas posted the more generic way to make a SymbolList from a string and an
alphabet.

> 4. Does anyone on this list know about the Bio-OpenSource meeting at ISMB
> '00, and what will be taking place there?  The ISMB web-site is kind of
> vague about it, but the registration deadline is fast approaching.

I will be presenting BioJava (which alone should make it worth visiting). There
are many other exciting presentations planned. I have pasted in the mail which
contains a usefull URL, and a list of things that are happening. I hope that
helps make your mind up :->

All the best,

Matthew

>
>
> Thanks in advance,
>
> Michael Giddings, Ph.D.
> University of Utah, Dept. of Human Genetics
>
> * For those not familiar, Objective-C inherits most (if not all) it's
> semantics from Smalltalk, and it is also semantically quite similar to Java.
>
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l

Subject:
          [Bosc-attendees] BOSC'2000 Schedule & Speakers (v1.0)
***
Please note that this initial schedule is subject to change.
Revisions will be posted on the meeting website,
http://ismb00.sdsc.edu/bosc2000/
***


The Bioinformatics Open Source Conference (BOSC) is the followup to the
successful bioperl-99 workshop, which was also a satellite conference
of ISMB.  BOSC encompasses all the open source efforts in bioinformatics,
including but not limited to the BioPerl, BioJava, BioXML, and BioCORBA
projects.  The meeting focus is on software engineering techniques in
the life sciences, with a particular emphasis on open source software.

Generous donations to help offset BOSC organizing costs have been
made by Compaq Computer Corporation and Congenomics Inc.

The BOSC 2000 Organizing Committee is:
Ewan Birney (EBI)
Chris Dagdigian (Genetics Institute)
Nomi Harris (Berkeley)
Helge Weissig (UCSD)

BOSC 2000 committee email:
bosc@bubbles.sonsorol.org

BOSC 2000 Schedule

August 17th:
1:00-2:00       Registration and poster setup
2:00-2:20       Intro/Bioperl (Ewan Birney, EBI)
2:30-2:50       BioJava (Matt Pocock, Sanger Centre)
3:00-3:20       BioXML (Brad Marshall, Berkeley)
3:30-4:00       Coffee break
4:00-4:20       BioPython (Jeff Chang, Stanford)
4:30-4:50       BioCorba (Jason Staitich, Duke)
5:00-5:20       Ensembl (Michele Clamp, Sanger Centre)
6:00          Dinner @ UCSD
8-10pm        Ad hoc meetings & BOF gatherings


August 18th:
9:00-10:00  Keynote talk by Tim O'Reilly
            (O'Reilly & Associates)
10:00-10:30 Coffee break
10:30-10:50 Distributing bioinformatics applications with Piper
            (J.W. Bizarro, University of Massachusetts Lowell)
11:00-11:20 Exploiting emerging open I/O protocols for high-throughput
BioAnalysis
            (Lawrence Lau, University of Queensland)
11:30-11:50 An introduction to Genome Annotation Markup Elements (GAME) XML
            (Suzanna Lewis, Berkeley Drosophila Genome Project)
12:00-2:00  Lunch and poster session
2:00-2:20   A distributed annotation system client
            (Robin Dowell, Washington University, St. Louis)
2:30-2:50   Telegraph: A free library for probabilistic sequence analysis
            (Ian Holmes, Berkeley Drosophila Genome Project)
3:00-3:30   Coffee break
3:30-3:50   E-CELL: Simulation environment for white cell simulation
            (Kouichi Takahashi, Keio University)
4:00-4:20   FAKtory: An Open Source DNA fragment assembly system
            (Susan J. Miller, University of Arizona, Tucson)
4:30-5:15   Keynote talk by Lincoln Stein
            (Cold Spring Harbor Labs)
5:20-5:30   Closing remarks / End of 'official' BOSC'2000 meeting
5:30-??     Open forum on legal implications of Open Source


Abstracts for talks and posters will soon be available at
http://ismb00.sdsc.edu/bosc2000/




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