nodalpoint.org

Scientists usually share information with collaborators from all around the world. For that purpose, eyeOS (www.eyeos.org) provides an invaluable system to access and share documents, create and save data files or store crucial personal and professional information.

To see eyeOS widely used by scientists all around the world, we initiated the eyeLIMS project ! eyeLIMS is a community-driven project which aims at providing a Free, web-based, Open Source Laboratory Information Management System (LIMS) powered by eyeOS.

After a long hiatus SciView is back with a new interview with Dr Roderic Page from the University of Glasgow. Dr Page is the current Editor in Chief of Syatematic Biology and developer of TreeView(X), the beloved phylogenetic tree visualization software. He was also the editor of the Current Protocols in Bioinformatics.

As usual here is the link.

Enjoy.

What's the best way to discuss "open research"? Let's say that you have a research problem. You might post it on your blog and receive comments. Or you might create a wiki with questions, to which people can contribute answers. All well and good, but then we end up with useful content spread all over the web. What's the solution? Centralised portals, aggregators? Or are people happy to search multiple sources for content?

I don't know the answers. However, in the spirit of Mike's open science article on our wiki, I created an open research section. The idea is that if someone performing open research has a question and you have an answer, you can post it here and point them to it. I've kicked things off with a look at a recent bioinformatics problem from Rosie's blog.

I'm not proposing that this be the central point for these kinds of discussions - it's just another alternative and one that we can all find.

The paper described a framework for comparisons across gene expression microarray platforms and laboratories, which including: 1) Affymetrix; 2) Agilent; 3) Applied Biosystems (ABI); 4) Amersham (now GE Healthcare); 5) cDNA arrays provided by the Cepko laboratory (academic cDNA); 6) Compugen (now Sigma-Genosys); 7) Mergen; 8) long oligonuceotide arrays from the Microarray Core facility at Massachusetts General Hospital (MGH long oligo); 9) MWG BioTech (now Ocimum Biosolutions); 10) Operon. As a result, the commercial platform ABI has the best performace, where the academic cDNA from Harvard poorest.

I'm the founder of The Synaptic Leap We're also using Drupal. Our site has been live since late November. I'm coming out to the SF Bay Area May 30 - June 6. Is anybody maintaining NodalPoint interested in getting together to discuss possible synergies and philosophies?

Email me or reply to the post to discuss.

This is an announcement of a bioinformatics tool, published as freeware for the community.

Geneious is an easy-to-use, cross-platform (Windows, OS X, Unix) bioinformatics data analysis and visualization tool. It has an open API for writing plugins. You can use Geneious to compare genes from different species, to build an evolutionary tree to see how closely related they are, or to search for literature on any topic in medicine or biology. You can view and extract gene annotations from whole genomes, and interactive 3D graphics allow you to move around protein structures.

Version 1.0 of Geneious has just been published as freeware. Biomatters hopes that you will put the program to good use in your research, and we are eager to hear your comments and feedback.

Enfold Systems just released a Open Source LIMS based on Zope 3 (written in Python) and the python Object/Relational module, SQLObject.

SIP's Project Page is at the enfold systems website. It has flash demo's, screenshots and a link to Sample Inventory Program's Sourceforge Prroject It uses Postgresql but should work on MySQL and on Windows, OSX or *BSD. Link to download 1.0.2

The SIP application requires the Zope 3.0.x release of the Zope application server, PostgreSQL or Sybase Relational Database Servers and the Python 2.3.5 language runtime. Many integration tests exist for various aspects of the SIP application ranging from command line importing of samples and project configuration to CSV web based importing of sample modifications.

I have been noticing that Nodalpoint's "Who's online" box has been showing somewhere in between 20 to 80 people online at any given time and this got me thinking again on how internet has been such a strong positive force for the development of collaborative work. Open source software comes to mind as one of the best examples of what you can achieve by getting interested people together in a virtual space. Why can't we do the same for scientific research ?

The first issue of PLoS Computational Biology is out. The journal's editors want this to be one of the main forums for the people working in the field of computational biology but so far what I would say is that it is nice to have another open access journal where we can aspire to publish our work.
I would like to point out the interesting perspective by Sean R. Eddy. Among several other interesting points he argues for interdisciplinary people instead of interdisciplinary teams and how the recent "big science" mentality might actually hinder innovation.

Please reveiw my website

src = "http://www.bioinfo.co.nr"