9 replies to this topic

[maestro949]

Thread to store tools of interest for building bioinformatics stuff. Designing schemas, code, etc.

Case Studio 2 (ER Modeling)

PostGreSQL (Database)

Java 1.5

Eclipse

Apache Tomcat (JSP/Servlet Engine)

Apache Axis (Distributed SOAP Engine)

Microsoft Visual C#

Edited by maestro949, 12 June 2006 - 07:08 PM.

[maestro949]

Eclipse Pathway Editor

[emerson]

I couldn't think of much more to add, but the mention of java started up a kneejerk reaction to mention the Java 6 JDK snapshots. Good for a production release, hell no. But a lot of fun to play around with. The GTK L&F actually comes out appearing fairly acceptable in linux!

[caston]

A quick search on sourceforge.net gives 104 results:

http://sourceforge.n...=bioinformatics

Of course source forge being source forge you may be lucky to find a handful of usable projects. I have yet to try any of them.

[maestro949]

Check this out caston...

LifeSciences Projects

Personally I'm trying to project 5-10 years out as I have a lot of science still to learn but here's my optimistic prediction:

1. Most of the proteome will be mapped as an enormous data set
2. Rudimentary first generation cell simulators will have evolved (literally) from the work being done today in molecular dynamics and protein folding and todays pathway and limited cell simulations.
3. Genetic algorithms and molecular docking algorithms for de novo drug design will merge into tools that allow systems bioengineers to model multi-compound designs that test multiple gene expression alterations simultaneously.

Fighting aging will largely mirror the fight on cancer. Tools that evolve for searching/testing/screening cancer treatments will lend themselves well to repairing the genetic network alterations and physiological damage that accumulates during the aging process. I suspect that most of our time will be focused on the search for molecules that trigger gene expression to up or down regulate.

The bioinformatics stuff that is floating around currently is interesting but I suspect something more impressive will likely evolve out of universities/open source community or be dropped on us from one of the 800 lb gorillas, e.g. IBM life sciences group, Novartis or even a consortium of many of those mentioned.

[maestro949]

Oh yeah, we'll need Subversion Source Control

[maestro949]

I couldn't think of much more to add]Java 6 JDK snapshots[/URL]. Good for a production release, hell no. But a lot of fun to play around with. The GTK L&F actually comes out appearing fairly acceptable in linux!

Java on the desktop....*sigh*

Poor SUN. I don't think they'll ever get it right.

[emerson]

Poor SUN.  I don't think they'll ever get it right.

It's almost embarrassing to admit it, but I have to say that I actually have been enjoying using swing lately. I have a bad habit of being overly perfectionistic in GUI design, but at the same time incredibly lazy about it, especially when it comes to tweaking for platform differences. The java6 and matisse combo have been a pretty good compromise so far. Also nice for having a single file I can throw onto flash and run on the handful of computers that I move around on.

That said, I have to second both the opinion and sentiment. The sheer size of some of the mistakes Sun's made, or opportunities just tossed to the wind, are insane. To the point of being almost endearing in a way. I always get this vision of 500 different red tape coated brains commanding a single body to move in different directions at the same time.

[maestro949]

I have seen some good swing apps recently but IMO it's too little too late. After 15 or so years of trying Microsoft has finally gotten it right with Visual C#. Still buggy as hell but the UI dev environment + 3rd party libraries allows you to snap together sharp looking apps fairly quickly. Thanks to Moore's law they actually perform on a reasonably priced PC.

[maestro949]

Some Genetic Algorithm Packages for Java

ECJ - Evolutionary Computation/Genetic Programming research system

Java API for Genetic Algorithms

n-genes Java 5 GPL Genetic Algorithms and Programming Toolkit

JGAP - Java Genetic Algorithm Package


Multicast Tech

The Java Reliable Multicast Service[tm] is a set of libraries and services for building multicast applications. It enables building applications that multicast data from senders to receivers. The JRM Service supports multiple reliable multicast transports through a federated interface, which provides isolation to applications, and a service provider interface underneath to allow third parties to plug in other reliable multicast transport implementations.


Java Reliable Multicast Service