nodalpoint.org

It seems that the emperor has no clothes:

The utility of ontologies has been clearly demonstrated in several biological domains (e.g., Gene Ontology). However, within biology, the enthusiasm for ontologies has been accompanied by a general lack of awareness of what exactly ontologies are and how to use them.

This is from another Semantic Web related Nature article: Are the current ontologies in biology good ontologies?, via Julio Bonis. The point the authors are trying to make is that many of the current bio-ontologies are poorly designed and are therefor unsuitable for use in knowledge sharing applications and automated reasoning (i.e. Semantic Web). They put the MGED microarray ontology under the microscope, finding many inconsistencies.

When I first started learning something about sequence analysis, I looked for -- but couldn't find -- a "no learning curve" Java class library to get me started.

Based on that experience I wrote, and just posted, a library of Java foundation classes for sequence analysis at hannohinsch.com/javagene Very simple, very clean. Fully documented with JavaDoc and sample programs.

Great for student projects, and research too.

A work proposal over DNA regulation.
I would like to scan OMIM for human diseases caused because of regulatory disturbances. I would like to classify these diseases based on the levels at which the problem has occured such as chromatin sturcutre, initiation, trasncript processing, transport to cytoplasm, translation of mRNA, stability of mRNA and stability of the protein activity itself. The goal is to find the patterns emerging in these regulatory regions which lead to normal functioning/disease of the system.
If any of you has idea of what I am talking and is interested, I would like to get in touch with you and start this work.

Via the Semantic web life sciences list: A Nature Biotechnology Perspective disucssing the importance of Semantic Web Technologies and their impact on 'omic standards, is available online (I was able to access this from home ? But a subscription may be required, which is really starting to annoy me). I just don't understand how anyone is supposed to discuss science online if all the information is locked up in walled gardens ?

Anyway the article is good, it is long, but worth the read if you care about how you spend your time doing bioinformatics or if you want to see what the future has in store for biological standards development. So now that you've taken the trouble to read the article and attempted to digest the significance of it, you're probablly thinking "So what ?" it has no real practical benefite for me now ?

It is true that articles like this do not explain these technologies from the point of view of the "working bioinformatician" i.e. what is in it for me if I bother to investigate RDF now ? Read on for some working examples of RDF data integration and a few thoughts on the future of the semantic web and the life sciences (warning, this is an article not a post, so grab a beverage or something).

Remember SARS? It came, there was a wealth of "end of the world is nigh" TV documentaries, some guys in Canada sequenced it over a weekend...and then it was yesterdays news.

The latest BMC Genomics contains an article (link) which claims that the clinical severity of SARS correlates with the expression of around 52 signature gene transcripts from whole blood samples.

I am no expert in the array analysis methods that they've used or medicine in general, but it looks interesting.

Hi, I have a question and I don't know a generic bioinfo-mailinglist where I could ask it: I wonder if there exists a program that does _partial_ assembly from shotgun sequences like those in trace-files (e.g. traces.ensembl.org). As a biologist, you often need only part of a genome that you're interested in. You have some similar sequence, the damn organism is even sequenced, but not assembled yet. Now, how the heck can you get a long sequence out of the trace archives?

OK, I am about to simply run blast, collect all the sequences that I get, clean vector contamination, assemble them with CAP3. With this kind of longer sequence, I can run blast again, clean, assembly, etc... and iteratively extend my sequence in to both direction, finally having my gene of interest complete from the trace archives. Without the need for a supercomputer. OK, now I just have to hack together this script.
Does it already exist? I guess I am not the only one who is hoping that a certain trace archives might come to the rescue....

As a card-carrying geek, I don't do anything so pedestrian as PubMed searches. Instead, I have Hubmed deliver common search content via RSS (cheers, alf!). A side effect of this system is that you see a lot more literature than you otherwise would, particularly for broad-brush searches. In some cases, this may be instructive, leading you to things that would have escaped your notice otherwise. In other cases, it leads you to the plain weird. As a case in point, a search for "regulatory variation AND mammals[mesh]", one of my standards, today popped up with this:

A new Journal list on Bioinformatics, as a guide to publication and reference in my bioinformatics study life and research work.
Nature
Science
Nature Review Genetics
Nature Genetics
Nature Biotechnology
Nature Molecualr System Biology
PLoS Biology
PLoS Genetics
PLoS Computational Biology
PNAS
Journal of Proteome Research
Genome Biology
Genome Research
Genomics, Proteomics & Bioinformatics (GPB)
Applied Bioinformatics
Artificial Intelligence in Medicine
Artificial Intelligence
Bioinformatics
BMC Bioinformatics
BMC Medical Imaging
Briefings in Bioinformatics
Chemometrics and Intelligent Laboratory Systems
Computerized Medical Imaging Graphics

Data Mining and Knowledge Discovery
Healthcare Informatics
Healthcare Information Management and Communications Canada
In Silico Biology
International Journal of Medical Informatics
Journal of Biomedical Informatics
Journal of Chemical Information and Modeling
Journal of Computational Biology
Journal of Machine Learning Research
Journal of Molecular Graphics and Modelling
Journal of Molecular Modelling
Journal of Structural and Functional Genomics
Journal of the American Medical Informatics Association
Journal of the Medical Library Association (JMLA)
Machine Learning
Metabolic Engineering
Molecular and Cellular Proteomics
Nature Structural and Molecular Biology
Nucleic Acids Research
Online Journal of Bioinformatics (OJB)
The Online Journal of Issues in Nursing
Protein Engineering
Protein Science
Proteins: Structure, Function, and Bioinformatics
Structure

Found this place through google, I will use it as a jouney to my research.

I was recently alerted to a policy regarding media coverage of CSHL meetings that I was totally unaware of. Via this exchange on Notes from the Biomass (nice title by the way):

greg - 2005-09-16 13:01
And highlights so far are ?

In reply:

spitshine - 2005-09-16 14:25
Difficult to answer really: For one, Cold Spring Harbor Meetings have strong policy on media coverage of the conference, considering all presentations and posters personal communication. Guess blogging the content would not be a good idea.

So does that mean I was in violation of ISMB's press policy, when I recently blogged sessions I attended ? I did some investigating...