nodalpoint.org - Bioinformatics - Comments

User-friendly, High compatibility but low requirements

amejat — Tue, 06 May 2008 17:37:22 -0400

Hi Neil,

And thanks for your interest in the project. I fixed the mistake in "invaluable".

I also completely agree on the facts that:
- we need a free open source Laboratory Information Management System
- to be adopted, it needs to be user-friendly, cross-platform, highly compatible with existing open source solutions.

I had that in mind when I joined the eyeOS team, three years ago and I always kept it in mind during eyeOS development. And it is because eyeOS fits these needs that I really think it provides the perfect platform for a LIMS:
- For users, eyeOS provides a really intuitive and user-friendly desktop-like environment, accessible from anywhere.
- For developers, eyeOS provides a complete Toolkit and set of libraries to easily and quickly develop new eyeOS applications.
- For network manager, eyeOS has very low requirements. It only needs PHP and XML (javascript being provided by the navigator). It does NOT require a MySQL (or other) database or a Java server (such as Tomcat). For this reason, it can be installed on any basic hosting plan. However, it allows the easy integration of Flash (swf), Java applets or MySQL applications. Importantly, it constitutes a secured platform to store and share documents with a Virtual File System controlling the user access to files.

To conclude, the last but not the least, eyeOS is Free and Open Source. To my knowledge, it is unique.

I hope you will take time to discover this platform and agree with me on its potential.

Best regards,

Alexandre

www.eyeLIMS.com - Free Open Source Laboratory Information Management System powered by eyeOS

Value

Neil — Tue, 06 May 2008 02:55:35 -0400

provides an unvaluable system

*Invaluable*, surely. I hope?

I'll be interested to see how this develops: the research world is in desperate need of a quality, open-source LIMS. However, I'm concerned that this LIMS is tied to an existing product. Everyone has a web browser, but not everyone will want to sign up for eyeOS and learn how to use it. A true web application is something more like Google Documents, where you just open a page and start work.

Remember, biologists will look for any excuse not to learn how to use an application; you need to keep the entry barrier as low as possible.

simulaid

bosco — Thu, 16 Aug 2007 13:23:16 -0400

I downloaded it but couldn't get it to work properly for NAMD to AMBER.

Simulaid

Animesh — Thu, 16 Aug 2007 10:46:02 -0400

I have no idea about converting trajectories, but people talk about using Simulaid [ http://inka.mssm.edu/~mezei/simulaid/ ] for similar stuff, did you check it?

Looks familiar

Neil — Wed, 15 Aug 2007 09:52:19 -0400

Good to see that file format conversion is a full-time preoccupation in structural biology as well as for people working with sequences. Nice how-to.

Sure

nuin — Wed, 15 Aug 2007 07:48:40 -0400

The more the better.

I am in the process of finishing a manuscript and we will start coding as soon as I finish it. I send you an email with the idea.

BTW, pretty nice application you have.

Paulo

Need some help guys?

bosco — Wed, 15 Aug 2007 03:03:43 -0400

I'd love to help out even though I'm just a structural biologist and not a sequence jockey.

I have experience programming in C++/wxWidgets: I've written a complete GUI application in that platform http://boscoh.com/ramaplot. My main platform @work is Python so I'm keen to seen how wxPython stacks up against wxWidgets.

I can help you work on the GUI aspect.

Just a wild guess, but I'm

Greg — Tue, 14 Aug 2007 14:11:00 -0400

Just a wild guess, but I'm thinking this particular piece will not have the same broad impact of "Notes to a young computational biologist". Nonetheless, I am thinking that maybe your posts on these topics have brought a few more structural biologists into the world of blogging :)

Nightmares

mndoci — Tue, 14 Aug 2007 14:09:44 -0400

And I shudder at the memories of trajectory formats.

We should start a movement for MD standards, as in Force Field standards, trajectories, etc etc.

Sorry

nuin — Sun, 12 Aug 2007 09:30:01 -0400

My bad, forgot to post the most important thing!

Cheers

Link to interview

Neil — Sat, 11 Aug 2007 23:21:43 -0400

The interview itself is here.

String-blasting

Bob Carpenter — Wed, 20 Jun 2007 13:01:43 -0400

It's useful to apply BLAST-like techniques for searching over strings. This has been used to find variations of the names of genes in text by several groups. First, Michael Krauthammer, when he was at Columbia, used base-pairs to encode arbitrary strings (they're usually encoding amino acids), then queries gene and protein names for matches in the text of journal articles.

BLAST is really just edit distance with some exclusion heuristics which don't work at all well on small strings. So it's more natural to implement this notion directly, as Tsuruoka and Tsujii did. There's a nice description of the algorithms in Dan Gusfield's string algorithm bible.

Our LingPipe software provides an implementation of approximate dictionary matching following Gusfield. Here's a link to the class Javadoc: com.aliasi.dict.ApproxDictionaryChunker. We provide Tsuruoka and Tsujii's distance metric as a constant, but the distances are plug-and-play.

The really critical issue here is not just finding approximate matches of names of biomedical entities, but also disambiguating them. The acronym "ACT" means a lot of different things in different contexts. Figuring out which sense of a word or phrase is intended is a widely studied problem usually going under the heading of word sense disambiguation for common nouns or database linkage for proper nouns. This can either be done via unsupervised clustering, or by supervised database linkage if there are example contexts. Luckily, databases such as Entrez and KEGG provide GeneRIFs which include pointers to articles about specific genes. And evaluations like Biocreative are evaluating abilities of systems to figure out which gene is being mentioned in an article.

Bob Carpenter

Alias-i, Inc.

Flawed, but useful analogy: Bloogle

Duncan — Mon, 18 Jun 2007 07:29:40 -0400

I think Google is still a useful analogy for explaining BLAST to wet bench biologists, even if it does have its flaws. As for "Google isn't statistical", I disagree. What about all that statistics, probability and machine learning they use to builld and improve search results? Google (and other search engines) have very well defined metrics for measuring search quality, it's not all subjective. So despite its problems, search is still a handy analogy for describing BLAST that many people will be familiar with.

Analogy

Jonathan_Badger — Mon, 18 Jun 2007 07:02:50 -0400

Or, BLAST is like a microwave oven, except for sequences and not frozen burritos.

But seriously, I think the Google analogy isn't very good because
1) You don't search using a subject in BLAST, but by using another sequence. If Google worked that way, you'd give it a web page and it would find web pages similar to it.
2) BLAST is statistical, Google isn't. The only measure of how good a Google search is is the (subjective) opinion of the searcher.

If you want an analogy, assuming the students know some bench biology, how about "BLAST is an electronic Southern Blot"?

more on pathways

vndinu — Sat, 16 Jun 2007 17:45:22 -0400

Interesting comments, some of the commercial pathway analysis tools are indeed quite good. I'm also working on a pathway-based analysis of genotype data, the paper is in press in the Journal of Biomedical Informatics and the tool will be made publicly available soon. valentin dinu, http://www.dinuinformatics.info