From dlondon at ebi.ac.uk  Tue Apr 19 05:16:30 2005
From: dlondon at ebi.ac.uk (Darin London)
Date: Tue Apr 19 06:55:23 2005
Subject: [DAS] Re: BOSC 2005
In-Reply-To: <20050120175859.GA7254@parrot.ebi.ac.uk>
References: <20050120175859.GA7254@parrot.ebi.ac.uk>
Message-ID: <20050419091628.GN17377@parrot.ebi.ac.uk>

{Please pass the word!}

SECOND CALL FOR SPEAKERS
 
The 6th annual Bioinformatics Open Source Conference (BOSC'2005) is organized by the
not-for-profit Open Bioinformatics Foundation. The meeting will take place
June 23-24, 2005 in Detroit, Michigan, USA, and is one of several Special Interest
Group (SIG) meetings occurring in conjunction with the 13th International Conference
on Intelligent Systems for Molecular Biology.
 
see http://www.iscb.org/ismb2005 for more information.
 
Because of the power of many Open Source bioinformatics packages in
use by the Research Community today, it is not too presumptuous to say 
that the work of the Open Source Bioinformatics Community represents 
the cutting edge of Bioinformatics in general. This has been repeatedly 
demonstrated by the quality of presentations at previous BOSC conferences.
This year, at BOSC 2005, we want to continue this tradition of excellence, 
while presenting this message to a wider part of the Research Community.  
Please, pass this message on to anyone you know that is interested in
Bioinformatics software. 
 
 
BOSC PROGRAM & CONTACT INFO

* Web: http://www.open-bio.org/bosc2005/
* Online Registration: https://www.cteusa.com/iscb4/
* Email: bosc@open-bio.org

FEES


* Corporate : $195 ($245 after May 16th)
* Academic : $170 ($220 after May 16th)
* Student : $145 ($195 after May 16th) 

SPEAKERS & ABSTRACTS WANTED

The program committee is currently seeking abstracts for talks at BOSC 
2005. BOSC is a great opportunity for you to tell the community about 
your use, development, or philosophy of open source software development 
in bioinformatics. The committee will select several submitted abstracts 
for 25-minute talks and others for shorter "lightning" talks. Accepted 
abstracts will be published on the BOSC web site.

If you are interested in speaking at BOSC 2005, 
please send us before April 26, 2005:

* an abstract (no more than a few paragraphs)
* a URL for the project page, if applicable
* information about the open source license used for your software or 
  your release plans.
 
Abstracts will be accepted for submission until April 26, 2005.
Abstracts chosen for presentation will be announced May 12, 2005 
(before the ISMB Early Registration Deadline).
 
LIGHTNING-TALK SPEAKERS WANTED!

The program committee is currently seeking speakers for the lightning 
talks at BOSC 2005. Lightning talks are quick - only five minutes 
long - and a great opportunity for you to give people a quick 
summary of your open source project, code, idea, or vision of the future.
 
If you are interested in giving a lightning talk at BOSC 2005, 
please send us:
 
* a brief title and summary (one or two lines)
* a URL for the project page, if applicable
* information about the open source license used for your software or 
  your release plans.
 
We will accept entries on-line until BOSC starts, but
space for demos and lightning talks is limited.<br/
   
SOFTWARE DEMONSTRATIONS WANTED!
If you are involved in the development of Open Source Bioinformatics Software, 
you are invited to provide a short demonstration to attendees of BOSC 2005.
 
If you are interested in giving a software demonstration at BOSC 2005,
please send us:
 
* a brief title and summary (one or two lines)
* a URL for the project page, if applicable
* Internet connectivity requirements (e.g. website Application served on the 
  world wide web, or web based client application).
 
  We will accept entries on-line until the BOSC starts, but
  space for demos and lightning talks is limited. 
 
 ** Because the mission of the OBF is to promote Open Source software, we will favor submissions for
  projects that apply a recognized Open Source License, or adhere to the general Open Source Philosophy.
  See the following websites for further details:
  href="http://www.opensource.org/licenses/
  href="http://www.opensource.org/docs/definition.php
 
 
 SESSION CHAIRS WANTED
 If you would like to be involved BOSC 2005, we invite you to chair a session.  This will 
 not require much of your time.  You will be given a schedule of presenters during your session. 
 You simply introduce each speaker, and manage the time of their presentation (25 minutes for full 
 presentations, 5-10 minutes for lightning talks/demos, depending on the number of entries).
 
 If you are interested in chairing a session, please send us your name and affiliation (if applicable).
 
-- 
cheers,

Bosc Organizing Committee
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From LSimirenko at lbl.gov  Tue Apr 26 17:25:18 2005
From: LSimirenko at lbl.gov (LSimirenko@lbl.gov)
Date: Tue Apr 26 17:18:49 2005
Subject: [DAS] help with Dazzle LdasDataSource
Message-ID: <1c9b381c6256.1c62561c9b38@lbl.gov>

Hi,
I am a newbie, trying to set up a das annotation server.
I chose Dazzle because I am already using tomcat for other webapps.

I would like to use a mysql database to store the annotations so I set 
up an LDAS type mysql database and loaded it with some test data,
but I don't think I configured dazzle properly, or I may not have the 
permissions set properly in mysql.

Is there any documentation on how to use the LdasDataSource type in 
Dazzle?
and/or the best way to troubleshoot the configuration?

Thanks,
Lisa
Here is a snippet from my config file:

<datasource id="bcdBRs" 
jclass="org.biojava.servlets.dazzle.datasource.LdasDataSource">
    <string name="name" value="bcdBRs" />
    <string name="description" value="Bicoid Binding Regions" />
    <string name="version" value="default" />
    <string name="dbURL" value="jdbc:mysql://simi.lbl.gov/dicty" />
    <string name="dbUser" value="nobody" />
    <string name="dbPass" value="" />

    <string name="mapMaster" value="http://genome.cse.ucsc.edu:80/cgi-
bin/das/dm2" />

    <string name="stylesheet" value="bcdBRs.style" />
  </datasource>



From suzi at fruitfly.org  Wed Apr 20 18:42:29 2005
From: suzi at fruitfly.org (Suzanna Lewis)
Date: Fri Apr 29 07:21:43 2005
Subject: [DAS] Hackathon 2005
Message-ID: <a461b8d8e0fdc21c10105bd3207e45ce@fruitfly.org>

(sorry for multiple postings, but please do forward to
anyone else who you think might be interested)

------------------------------------------------------------------------ 
-----------

Dear everyone,

It has been a long time and we Bioinformatics devotees are overdue for
another total-immersion coding-fest (the last hackathon was held in
Singapore February 2003, more than two years ago).  Apple has offered
to host us this year, and as an added bonus include free admission to
the World-Wide Developers Conference in San Francisco the prior week.
They are also looking for some people to present interesting new
developments at the WWDC, so if you have something noteworthy please
let us know. Apple is not attaching any strings, so our work need not
address Apple-specific software or hardware areas. Apple will provide
space and hardware (and access to their engineers if we'd like).

Week 1 (June 6-10) would be spent at the WWDC. Week 2 (June 12-16)
would be in Cupertino, at Apple's headquarters.  We're free to focus
on what interests us, our tentative plans include:

   1. Bio-ontologies software
   2. High-performance computing (e.g. large scale computations,  
optimization)
   3. Image analysis
   4. Documentation
   5. Anything else that may interest you

Our plan is to organize this much as the Aspen Center for Physics
computational biology workshops were organized (for those old enough to
remember): A couple of presentations to start the day; collaboration
and coding afterwards; time for a bit of fun (does anyone else
cycle?), and discussions in the late afternoons and evenings.

Would everyone who is interested in attending please send us a short
description of what you would like to do, and perhaps other people who
you would like to work with. There is somewhat limited space, so we
will try to prioritize groups that have a clear focus and a need to
interact. We now this is very short notice, but we hope that there
will be enough interest to make it possible.

We are looking into additional funding support, to pay for travel
expenses, but this is still to be decided.

Looking forward to hearing from everyone.
George, Cyrus, Steve, and Suzanna (the Bay Area locals)