The OpenHelix Blog

Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don’t make it to a blog post. Here they are for your enjoyment…

• From BioMed Central article alert: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models (highly accessed, on my to-be-read list) [Jennifer]
• P-ter at Gene Expression shows the utility of a good genome browser by finding processed pseudogenes in a region that a study identified as a ‘short, novel, unspliced transcript’ using a genome browser. [Trey]
• Semantic Medline Prototype? [Trey]
• Interesting Nature article & I think access is free: Citizen science: People power [Jennifer]
  

I’ve got tomatoes on my mind, so summer must be coming. It seems every where I turn, I’m being reminded of tomatoes. Not the grocery store/hot house kind, but the fresh farmer’s market/back yard-grown kind with juice and flavor so plentiful that it runs down your arms and onto the sunny porch floor where you are having your lunch. At first it was just from my dad that I was hearing about tomatoes. He is an avid gardener, but lives ‘up North’ where the growing season is wedge in between the edges of winter. And although they’ve been having frost until just lately, he’s been reading about vertical gardening (to optimize land usage) and dreaming of his crop of tomatoes.

I guess I haven’t been helping his insanity any with the garden catalogs I share with him, or my tales of season here in the ‘sunny South’. But it seems it isn’t just Dad & me now – the insanity seems to be spreading. Last week the Sunday paper ran a story on bread salads & featured a tomato salad – I am glunking (as it is known in my family) as I type because my mouth is watering at the thought of a good tomato-bread salad. My last trip to my local farmer’s market didn’t result in any tomatoes, but they were selling tomato plants.

Even my BioMed Central e-article alert is conspiring to add to my tomato dreams. As I scrolled through the list of ‘latest research articles in my subject areas’, my eye was naturally caught by the article entitled “Tomato root transcriptome response to a nitrogen-enriched soil patch“. How could it not peak my interest with my summer tomato insanity, my past experiences in expression analyses, and even a brief stint in a rhizobial lab as a technician? And I’m glad my ‘tomato affliction’ lead me to this article – it is highly accessed, well written & interesting, in my opinion. Rather than doing their experiments on well controlled, hydroponically grown tomatoes the authors instead tried to replicate a more ‘real world’ nitrogen-enrichment scenario by using an apparatus to deliver a non-homogeneously localized dose of nitrogen (as often occurs during actual fertilizer application)  & then tracking the transcriptional response of the plants to it. I don’t know that I found any of the the publication’s results surprising, or unexpectedly enlightening, but I did like the way they did their controls & experiments. I also really liked the way that they explained their experiments. If you take a look at the paper (it is free to access), check out figure 1a. Some might say that the image is simplistic, but it so perfectly explains the key aspect of the experiment – what I called the ‘non-homogeneously localized dose of nitrogen’ which isn’t all that specific of a description on my part. In an instant this simple image endows so much understanding to the reader – there is no extraneous jargon, verbiage,  or detail to slow one’s comprehension of the meaning. Figure 1a is elegant because of its simplicity and ease of absorption, in my opinion. This level of presentation is rare in research publications, which are often so dry that to all but the most interested they are a plow. Why is simplicity so valued in ‘little black dresses’, but not communication? (Sorry, I’ve digressed from my tomato insanity to a different bee in my bonnet – I’ll try to get back on track…)

If you too are dreaming of summer vacation & all that it might have in store, check out the article cited below for a science geek bite of fresh tomato & ENJOY!

Ruzicka, D., Barrios-Masias, F., Hausmann, N., Jackson, L., & Schachtman, D. (2010). Tomato root transcriptome response to a nitrogen-enriched soil patch BMC Plant Biology, 10 (1) DOI: 10.1186/1471-2229-10-75

Recently Mary pointed me to this journal that came out this year, I thought I’d pass it on to you: BioData Mining. The journal is open access and housed at BioMed Central and the focus:

…all aspects of data mining applied to high-dimensional biological and biomedical data, focusing on computational aspects of knowledge discovery from large-scale genetic, transcriptomic, genomic, proteomic, and metabolomic data.

There are some interesting articles in there, for example, this one on a new software developed gene ontology based  clustering for microarray experiments. They publish papers on resources, methodologies and scientific results from mined data. Could be a journal to keep an eye on.

If you haven’t already seen it, open-access publishing either just made a jump backward or forward. The not-so-open access Springer publisher bought Biomed Central, the open access publisher recently. Open access publishing took a huge leap with the passage of a law last year that requires NIH-funded research to be open access and deposited in PubMed central within 12 months of publication. The law hasn’t not met resistence though. Perhaps Springer saw the writing on the wall, so to speak, and decided that buying BioMed Central was a good move in a world were open-access publishing seems to be gaining ground. Or…?  According the BioMed Central FAQ about the buy, BioMed Central publishing will remain 100% open access.

According to this BioMed Central blog, tomorrow is Open Access day – how shall we celebrate? Maybe read an extra open access article or two? Attend one of the events? Your blog on Oct 14th about the importance of open access to you could win you a ‘bag of swag’ PLoS ‘Synchroblogging competition – get writing this weekend’ competition. Another option is to join the BioMed Central Facebook fan club. As you can see there are LOTS of ways to support OpenAcess – let us know what you do to celebrate this important movement.

The Public Library of Science was founded in 2001 and published a letter urging publishers to open access to research published in their journals (I remember this letter being presented at an ISMB conference then). PLOS launched a series of open access journals when the response wasn’t particularly enthusiastic from the publishers. Those PLOS journals have had some success since, as have those at Biomed Central, another open access publisher.

There has been resistance from scientific publishers to the open access movement. Some fully opposing it, others like Nature Publishing Group’s official opinion is that it has no position, but that the business model is unproven and peer review an expensive endeavor. Nature has been experimenting with open source models though through the Molecular Systems Biology (an open access Nature journal) supporting self-archiving through public repositories, making an exception for papers reporting genomes and their open text mining initiative.

And now a new development: Wednesday, President Bush signed the Consolidated Appropriations Act of 2007 (H.R. 2764), which requires all NIH-funded published research to be deposited into PubMed Central (and thus open access) within 12 months of publication.