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.

What, exactly, is the point of Elsevier?

Duncan — Wed, 02 Apr 2008 07:26:07 -0400

I've been waiting for this special issue on semantic biomedical mashups for a while now. The latest scheduled production date is September 2008, which makes it exactly one whole year from Call for papers to publication. Damn thats quick, faster than a speeding glacier! Those hot hot research results must be popping of the printing press at an alarming rate!

Which makes me wonder, what, exactly is the point of Elsevier? Why does it take them so long to publish? Some, in the Open-Access publishing community have suggested this kind of publishing is a slow and expensive way to assign copyright to information that should be in the public domain, while lining shareholders pockets. As a young scientist, I'm completey baffled as to why it should take this long to shuffle a few emails and Word documents around the internet in order to publish.

Anyway, enough of the griping. Every now and then, a pre-print pops up in the Journal of Biomedical informatics feed from PubMed. So while you're waiting for Elsevier, you can read one of the first papers in the special issue below.

Carole Goble and Robert Stevens (year unknown) State of the nation in data integration for bioinformatics, Journal of Biomedical Informatics, officially published sometime before the heat-death of the Universe (but don't hold your breath). DOI:10.1016/j.jbi.2008.01.008, pubmed.gov/18358788

Free access to NSNPAS in PubMedCentral?

Duncan — Fri, 25 Jan 2008 04:12:22 -0500

Nature, Science and OUP Bioinformatics are all absent from this NIH list of Journals That Submit Articles To PubMed Central, more details from alf on hublog.

Talking of PubMedCentral, if you haven't seen it already Building a GenBank of the Published Literature published in Science back in 2001 is an interesting read, along with the responses tracked in PubMed.

Yeah, need to update my

ejain — Tue, 22 Jan 2008 19:47:42 -0500

Yeah, need to update my blog...

700?

nuin — Tue, 22 Jan 2008 13:18:11 -0500

At 700 a pop for an Action Figure?

Dude, Where's My NAR?

Duncan — Tue, 22 Jan 2008 13:09:27 -0500

Hello Maximillian, I wasn't attacking NAR, was just wondering about what proportion of the data is dead. It is an interesting technical challenge to find this out. It would also be useful to measure the cost of gathering noisy, redundant and poorly understood data in terms of wasted resources (people, time, money, computers, false positives etc). Perhaps somebody has done something like this already? Especially with all the irresponsible sequencing just for sake of it that goes on...

As for the physicists, I mentioned them for comparison. Like you, I doubt they will use 100% of their data either, but will probably use much more of it. However, they keep delaying switching their big machine on, which means they are still waiting for the data. That is, unless when they finally flip the switch on the LHC, we all disappear into a black hole, tombs and all :)

It doesn't matter, they got published

lbbros — Tue, 22 Jan 2008 06:46:50 -0500

Does it matter that large quantities of this data will probably never be used?

Probably not, as their authors are already happy enough to have those published, and then they can ~~stop mantaining~~ move on to another ~~project~~ publication. It is indeed a sad state of affairs.

Swiss Prot Databases / Action Figures

Duncan — Mon, 21 Jan 2008 18:12:33 -0500

Hi Eric, yeah even more redundancy there. Talking of SWISS Prot people, I'm just wondering when your Amos Bairoch action figure will be available in shops?!?! What are you up to now that you've moved on from SWISS Prot to Seattle?

Why NAR

maximilianh — Sun, 20 Jan 2008 10:59:14 -0500

I add the usual defense of the NAR databases: At least they are indexed by pubmed, so as there are biologists that are not used to checking in google if there are websites about their subject, they will find them quicker via NAR. The data is not dead, websites can always be exported. (I've made the experience that for smaller databses it's usually quicker to scrape the data from an html page with something like HTTP::Recorder than writing to the person responsible for the data to send you an sql dump.) In addition, people get papers for their databases like this and other people can cite the database properly, so NAR makes the web citable and advances someone's career a little bit. It already eases the transition from a traditional paper-based science to a more web-orientated world. Databases are peer-reviewed, so they don't contain complete crap, a paper in NAR assures some minimal quality. And a write-only database is better than none at all, at least someone has collected something and you can scrape it from its tomb.

I would just love to see a minimal requirement for a publication in NAR: They should all offer some simple text-based export, e.g. tab-delimited flatfiles. That could save me a lot of time...

Of course, large quantities of these data are never used and never read. But, heck, this is research, right? 90% will not be used in the end. It's not too different from those 500 alignments algorithms, 200 genomic analyses, hundreds of papers that describe "new" cloning strategies, yet another new gene, etc. I don't believe that the physisists use 100% of their 1,5 GB / sec either.

Also, think of all the

ejain — Fri, 18 Jan 2008 20:12:16 -0500

Also, think of all the redundant effort that goes into setting up the basic technical infrastructure each database needs (data storage, user interfaces etc)...

simple xml

Duncan — Fri, 21 Dec 2007 07:11:11 -0500

For REST style web services, WADL does the same kind of thing to simplexml at php.net, as far as I can see.

For SOAP+WSDL style services, it is currently much harder to create simple documentation, because as Tim puts it the WS-* stack is bloated, opaque, and insanely complex. I think it’s going to be hard to understand, hard to implement, hard to interoperate, and hard to secure.

php.net

alf — Wed, 19 Dec 2007 18:18:05 -0500

Ideally what I'd like to see is something like the function documentation on php.net (eg simplexml): each service would have its own page, with an auto-generated outline of the service (from the WSDL file) and a block of "official" documentation and examples, then other people would be free to leave their own comments, clarifications and sample code snippets below.

Searchable, annotatable database of services: Feta?

Duncan — Mon, 10 Dec 2007 12:49:34 -0500

There's three options for a searchable, annotatable database of services. What we have with Feta now, what Feta will become and what other projects are doing.

1. What we have with Feta today: Feta annotations are available programmatically via a Web Service interface, see Feta WSDL or you can browse the raw XML if you have the stomach for it. In the near future, there may be a SPARQL endpoint you can query too. As it stands, Feta is OK, but could be a lot better.

2. What Feta will become Feta is far from perfect and we hope to improve it in various ways. The WS4LS-Catalogue project led by Carole Goble here in Manchester and helped by Rodrigo Lopez at the EBI starts in February 2008 to build a better registry of Web services for the life sciences community. You can ask them for more details if you are interested.

3. Other projects If the current or future version of Feta doesn't do what you want, you can use BioMOBY. They've had a searchable annotatable database of services for a while now, one of their strengths is their PERL API which lets you register new services using terms from an extendable RDF ontology.

See Feta: A light-weight architecture for user oriented semantic service discovery by Phil Lord et al

Feta - controlled ontology for annotating web services

agbiotec — Fri, 07 Dec 2007 14:37:18 -0500

It seems to me that the whole point of Feta is to have a controlled ontology for annotating the input / output of the web services, so you can automatically plug things together in a workflow (Semantic web services). That's where the real effort saver comes from, because even if you have the inputs / outputs well documented, still you need to spend time figuring out the which ports you should connect between two web service components in a workflow. And that becomes hairy in a flow with many-many components !