nodalpoint.org - Comparative genomics - Comments

Author-ity: Medline articles written by a particular author

Klager — Tue, 01 May 2007 03:10:11 -0400

As long as authors work in separate fields, they can be separated using the Author-ity tool to sort Medline hits by similarity.

http://128.248.65.210/arrowsmith_uic/author.html

Torvik VI, Weeber M, Swanson DR, Smalheiser NR. A probabilistic similarity metric for Medline records: a model for author name disambiguation. JASIST 2005; 56(2): 140-158.

Good ideas, now we need details

Neil — Thu, 15 Feb 2007 22:54:11 -0500

I think the idea of a wiki for collaborative annotation appeals to a lot of people. The discussion around your post highlights the challenge: we have to go beyond the idea to the details of the implementation, i.e. the software engineering.

It would be hopelessly inefficient to rely entirely on manual annotation and the efforts of users. A wiki would somehow need to capture data from existing sources (sequence databases + automated annotation) and present it to the user for editing. There would have to be rules (ontologies) and a way to agree on a final annotation (voting? approval by an expert?)

I guess we're looking for a combination of the functionality of the IMG, the ideas of manatee (but not the implementation) and the philosophy of wiki.

Networks

PedroBeltrao — Tue, 13 Jun 2006 12:30:44 -0400

Two recent papers I found interesting in protein interaction studies:
Why Do Hubs Tend to Be Essential in Protein Networks?
They shift the usual view from essential proteins to essential protein functions and try to estimate the percentage of essential interactions in yeast.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae
This was a great curation effort (and very useful resource). The analysis is huge but they cover so many aspects that they do not go into a lot of details.

Endosymbiont evolution

Neil — Sat, 10 Jun 2006 10:26:20 -0400

That is interesting. There's a heap of plastid evolution work going on just now involving the genomes of algae and cyanobacteria. I'm sure that with a few more complete sequences and some clever people, we'll have a pretty complete understanding of the evolutionary history of endosymbiosis and plastids.

Software patents

dbodde — Sat, 10 Jun 2006 10:08:25 -0400

Software patents are important for developing the highest quality software. They create markets for public and private innovation in the field. And while paying a bit for software sounds awful--when the immediate prospect is paying nothing--no software is free. Bioinformatic software is paid for by the public dollar with little accountability for the results.

On the biological side ...

Spitshine — Fri, 09 Jun 2006 11:23:46 -0400

I noticed the sequencing of this peculiar algae with the smallest known nucleus.

The author ID movement grows

Neil — Wed, 26 Apr 2006 20:26:35 -0400

I wonder if Pubmed could use an identifier for each author

A good idea and one we've discussed before. The time is ripe for this idea.

What about an AuthorID (tm) ?

Serial — Wed, 26 Apr 2006 16:04:56 -0400

I wonder if Pubmed could use an identifier for each author. Of course this depend of the existence of a central file of the world's scientists, but that could be useful in this context, to remove all ambiguity when looking at homonyms.

ESL

Animesh — Tue, 18 Apr 2006 08:49:32 -0400

Well the title of ESL's publication can also be patterned as 'Sequencing and Analysis of some_organism/some_part_of_genome' but it gets through the biggies (journals)... I feel there has to be something more then just new work, it has to be a new work with a novel approach, atleast for biggies! Just a thought MMH, Greg, Neil...

Science parody

Neil — Wed, 12 Apr 2006 06:07:03 -0400

There should certainly be some PubMed filtering here. For a moment I thought it was some bizarre joke.

Depressing

PedroBeltrao — Wed, 12 Apr 2006 05:29:20 -0400

A bit depressing to see these publications by Katoh. I can always take it as a joke but there should be some mechanism to remove these entries from pubmed. I thought Pubmed evaluated journals before accepting to track them.

On slightly unrelated news, Microsoft just release a Pubmed/Google Scholar like product. It is called Windows Live Academic.

Firstly sorry for the delay

Greg — Mon, 10 Apr 2006 08:05:17 -0400

Firstly sorry for the delay in posting, I didn't check the submission queue over the weekend (I know it isn't optimal, but it works) and second, I made a few minor edits.

The simple answer is they publish in crap journals.

Katoh and Katoh also have an equally enthralling series of papers with the following template title: Identification and characterization of [species] [gene name 1] and [gene name 2] genes in silico. The so-called journals that these papers are published in are all from the same company, very dubious. For amusement value go grab one of their papers (pdf) and count how many of the papers they cite are their own (I counted 15 out of 31). And finally here is the man himself: Masaru Katoh.

Gaming the system ? Could they be more blatant ?

I think this should be

Greg — Thu, 02 Mar 2006 04:24:40 -0500

I think this should be re-posted in the Announcements forum.

moved

Neil — Fri, 08 Jul 2005 23:32:46 -0400

Just found this comment. We moved to mod_perl, the new link is here.

genome browser software

Anonymous — Fri, 08 Jul 2005 23:10:06 -0400

If dynamic and flexible whole-genome viewing is important to your project, I recommend taking a look at the Integrated Genome Browser, an open source viewer released by Affymetrix.

The URL for the project is:www.genoviz.org.

A Java Web Start version is available here:
www.affymetrix.com/support/developer/tools/download_igb.affx

I use this viewer for in-depth analysis of my own data sets. I load in my data and then use the "Load DAS" feature to populate the scene with data from the UCSC Distributed Annotation Server, which serves the same annotations available in the UCSC Web-based viewer. This lets me view my own annotations together with the public data, an essential feature if you are developing new annotation methods and need to be able to scan quickly through them. The Santa Cruz browser is a little too clunky for doing genome-scale viewing.