nodalpoint.org - 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.

How is bioinformatics influencing stem cell projects?

chris — Fri, 18 Apr 2008 12:43:33 -0400

Perhaps you can tell us how, in your mind, bioinformatics is speeding up stem cells projects. Then we can go from there...

RDFs

cariaso — Fri, 11 Apr 2008 22:45:40 -0400

I came across this old thread, and thought I'd point out that these days SNPedia does have the sacred RDFs thanks to the semantic-mediawiki.org extension. Today the most obvious benefit is that the SNPedia:FAQ is able to maintain some live counts about the site. The RDFs aren't yet connected to any others, but one baby step at a time it looks a bit more semantic. It seems only a matter of time until it can leverage SPARQL and perhaps the Halo browser.

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

BioBlogs 19: Bioengineering is here...

Duncan — Fri, 07 Mar 2008 05:18:49 -0500

So Bio::Blogs 19, the Bioengineering issue is out. Enjoy!

It's probably a bit late, but...

gpjt — Wed, 05 Mar 2008 07:35:32 -0500

Greg,

It looks like my colleague Jean missed your question - sorry for that!

Resolver One is now at version 1.0.1, and it's free for non-commercial use. For regular commercial use (online support in our forums, etc) it's $199 (reduced to $99 until the end of this month), and there is also a financial version with market data feeds, telephone support, SLAs, etc, on a rental model.

There's also a web server, which can serve up your spreadsheets as simple web applications - this is $699 (currently reduced to $499) per server machine, no client licenses required.

Regards,

Giles

Bioblogs: This is your last chance

Duncan — Wed, 27 Feb 2008 12:28:00 -0500

so if you're planning on sending anything to bioblogs /ate/ gmail.com for the latest issue of bio::blogs please do so now...

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.

R objects, and contacting authors

chris — Thu, 24 Jan 2008 10:27:34 -0500

I seem to recall that the limma/rma packages also have an option to return R and G values. Otherwise you can back-calculate from M and A.

M = log2(R) - log2(G)
A = 0.5*[log2(R)+log2(G)]

If only normalized data is available online, your best bet is to contact the authors and ask for raw intensities - there is no way of recovering them from processed data (at least, I don't think so).

They're cDNA data, according

lbbros — Thu, 24 Jan 2008 06:27:01 -0500

They're cDNA data, according to the paper (Zhao H et al., PloS Medicine 2005).

To tell you the truth, I'm not sure at all about consistency - but it's like a "test run" for a completely different approach I'm using: I'm just trying to see if such an approach is even feasible for the algorithm I'm going to run over the normalized data.

cDNA or oligo data ? Are you

Greg — Wed, 23 Jan 2008 11:42:14 -0500

cDNA or oligo data ? Are you sure the consistency of the data is good enough to be doing single channel normalization ?

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 :)