nodalpoint.org

maximilianh and alf suggested that we should try out and rate the tools in the 2006 NAR web server issue.
I've trawled through the abstracts and created this wiki page. With that much copying and pasting there are sure to be errors - I counted 146 links on the page, but then I'm now almost blind.

Anyway, the idea is that you can go there, choose a link and try it out, then leave a comment as to how well it worked for you. If you haven't used the Nodalpoint wiki before, it's dead easy. Just login with your Nodal user/password and look at some pages to get an idea of wiki syntax. I'm fairly sure that all Nodal users should be able to edit this but if not, leave a comment and we'll sort it out.

From Tim Bray to Jim Gray (via Seymour Cray)

Grid Computing already plays an important role in the life sciences, and will probably continue doing so for the forseeable future. BioGrid (Japan), ^myGrid (UK) and CoreGrid (Europe) are just three current examples, there are many more Grid and Super Duper Computer projects in the life sciences. So, is there an accessible Hitch Hikers Guide to the Grid for newbies, especially bioinformaticians?

Over at my little blog, I've been musing on how articles about web technology are entering the mainstream media. Examples include a recent SMH story on mash-ups (warning: fairly awful) and in the Guardian technology blog, a small piece on Google Trends.

Google Trends is quite addictive and informative. Try "bioinformatics" as a query - the trend for the past 2 years is rather interesting.

How the WSDL interface offered by a web service, will also help bridging the gap between CS and LifeSci,,, or otherwise between the IT-savvy biologists (aka bioinformaticians) and regular biologists.

You can get it at : BioIT - inside the box ...

If I am not mistaken, that something that's been going in the IT industry for some years now (SOA et similar stuff), for helping the expert and non-expert talking to each other.

This week's Nature continues the "new Web technology" theme with a look at wikis - specifically a comparison of Wikipedia and Britannica (with an editorial here).

I'm sitting in on the BioDASH demo, Eric Neumann is giving a broad strokes introduction to the semantic web, resources need metadata, basically if we can share and aggregate data and everything will be wonderful.

Now he's talking about semantic lenses, this I think is Haystack specific, he's talking about FOAF now. The slide he's using is the same one that was used in the bio-ontologies, for links see the comments here.

As discussed in a previous post, there is a sorry lack of open source LIMS (Laboratory Information Management System) software available.

I'm going to take the plunge and release a very alpha package to the world, called MamboLIMS. MamboLIMS is a LIMS package built using the Mambo Server CMS and 2 Mambo components - Peter Koch's fantastic Facile Forms package and DocMan for Mambo. The package contains 19 forms for managing many aspects of a biological research lab including a chemical inventory, fridge/freezer boxes, plasmids, microbial strains, oligos and book/equipment loans.

If you want to know more and try it out, read on.

I have just read an interesting article which discusses about the application of object-orientation paradigm, used in popular programming languages such as Ruby, Java or C#, in dynamical and statical description of different gene products and their derived forms. Object attributes and properties, which could refer to proteins and their ulterior complexes, come from vocabulary terms created in Gene Ontology initiative.
This is a very suggestion approximation, since it can unite the different ontologies and organization principles of GO (Molecular Function, Biological Process and Cellular Component) in the object context.
This enable, for instance, to use class diagrams generated with UML, in order to describe and simulate biological processes, and particularly, the interaction of their components.
I reproduce from the paper the correspondence between object-orientation principles and the integration of the model with Gene Ontology.

I have recently been put in charge of managing our department's -80°C cryostorage (ah the duties of a new PhD student...). Organization is chaotic: people come and go; they add new and forget old samples in the freezers... knowing what belongs to whom and whether or not we can toss it out can be impossible.

To ease department-wide, laboratory-wide and individual organization and tracking, we need a web-based system. Flexibility is the key word: some samples may be 1.5mL tubes of RNA hidden away in boxes and towers, and others may be whole birds or frogs. A superuser should be allowed to attribute space, while "simple" users should have complete control over their own space.

In Biomedical Digital Libraries journal, I have read an interesting paper which proposes unique identifiers for the authors of publications in Biomedicine.
This need comes from the growing amount of scientific publications, and the ever increasing difficult task of identifying the authors of those works.
Because of women incorporation in research and worldwide scientific contribution, the Anglo-Saxon inspired system of annotation based on a first name and one surname is not currently suitable for following authors trajectory. Things can get more difficult when authors may change the names they use along their lives. For instance, in some cultures, women usually adopt the surname of their husbands when they get married.
In order to show this, we can search in Pubmed Hernández A. and Lee C. These are not two very prolific researchers in different Biosciences fields, but simply, there are many people who may respond to this query.
Using a unique, unequivocal and personal identifier for each author, which could be centralized and registered in servers such as Pubmed (but preferably shared with other sites), could be a possible solution for this kind of problems.