Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.
In the continuing effort to get scientists and researchers to annotate and curate data and to capture the huge amount of knowledge available, UCSC Genome Browser has added a wiki annotation track to the browser. It’s not the first effort of course, GeneWiki is an effort, with mixed results so far, to annotate gene function information as a community exercise using Wikipedia. Some journals are requiring wiki entries, and several databases have opened wikis for curation. Wikis could be a solution for capturing the exponentially increasing amount of data,
or they could be just another place for adding confusion… or both. I suspect out of the plethora the wikis coming available for annotation and curation of genomic data, something will stick and find that Goldilocks balance of a dedicated community, ease of use, usability, and other aspects that will be needed for this to work.
Perhaps UCSC Genome Browser has that balance. It will remain to be seen, but let’s get started. Today’s tip is introducing the new wiki track in the UCSC Genome Browser.
I keep an eye on a lot of mailing lists. Usually they are the ones for database or software resources in our field. But I also keep an eye on some funding ones. We aren’t always eligible, but it also helps us to get a sense of the directions that projects are going.
Yesterday I saw one that surprised me on several levels. It is called BREAD funding. BREAD stands for Basic Research to Enable Agricultural Development. I found this one interesting because:
1. It is a joint project between NSF and The Gates Foundation. Maybe there are other federal funding projects that involve private foundations like this. But I haven’t seen them.
The National Science Foundation (NSF) and the Bill & Melinda Gates Foundation (BMGF) are partnering to support a new research program to be administered by NSF. The objective of the BREAD Program is to support innovative scientific research designed to address key constraints to smallholder agriculture in the developing world
2. It is giving money for plant genomics in agriculture. Cool! Among the possible directions for the research:
New strategies for creating resistance to major diseases and pests that affect plants, animals or insects of agricultural importance, and that have major impact in broad regions of the developing world.
3. It actually uses the phrase “climate change” and calls it a threat. And acknowledges several thing that I don’t think the last administration was serious about at all:
Novel approaches to using the genetic diversity of plants, microbes, or animals to enhance the ability of small-scale farmers to adapt to emerging threats of global climate change, emerging diseases, and the rising costs of energy.
Anyway, I’m delighted to see basic research on plants in agriculture in Africa and Asia getting some attention. I was pleased when I heard Hillary Clinton refer to this recently, but I was waiting for someone to show me the money. And what do you know–they did.
I am so behind in my reading lately, but I have several flights coming up so usually I get a lot of reading done then And there’s an important issue of Bioinformatics that I’ve been meaning to get to. I wish I had read some of it yet and had more insight, but right now you’ll have to go over for yourself and check out the articles.
It is a whole issue devoted to next-gen sequencing. You may not need to know or use every algorithm over there, but I’m sure there will be some excellent overviews and diagrams that can help you think about the issues in this field.
You are going to be seeing this data soon if you haven’t already.
Last night I had coffee with good friends in Davis Square and I mentioned that we had this blog. One of the friends (a linguistics scholar) seemed excited by the prospect until I told her the topic. She’s not nearly as excited by new software and scientific data as I am
It cracked me up this morning when I read the Reactome news letter–my first thought was: cool, axon guidance pathways! And I imagined my friend’s bemused look….
Anyway, there’s a new Reactome release. Here’s some of the new stuff content-wise:
New content. As part of a project to annotate the general process of cell motility and its involvement in key biological processes, Version 29 introduces a new topic, Axon guidance, with material now available for NCAM signaling in neurite outgrowth. Pathway topics updated with new curated events in this release include: Synaptic transmission (Glutamate Binding, Activation of AMPA Receptors, and Synaptic Plasticity), DNA Repair (regulation of FANCD2 and FANCI activity in the Fanconi Anemia pathway), and pathways whose dysfunction plays a major role in the development of diabetes (Regulation of insulin secretion and Unfolded protein response). With the annotation of G-coupled protein receptors (GPCRs) for eicosanoids, leukotrienes, nucleotide-like (purinergic) molecules, LPA and lysosphingolipids, opsins, secretins, and GABA and related molecules (class C/3 receptors), our annotation of interactions between GPCRs and their ligands is essentially complete. The Telomere Maintenance pathway has been revised in this release. Updated release statistics are available.
Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
You can keep up with this thread by remembering to check back, by subscribing to the RSS comments feed to this WYP post or by subscribing to be notified by email of new comments to the post (use checkbox at end of comment form, you can unsubscribe later). If you want to be notified of future WYP posts (every Thursday), you can subscribe to the WYP feed.
I’ve been reading a lot more on biodiversity lately, and I was really pleased to come across the Bioversity International site to learn more about this topic. Not a standard sequence or algorithm type of bioinformatics resource, the site is a collection of biological information on a wide range of topics and database resources that serve the needs of researchers interested in biodiversity. It’s really refreshing to see species that aren’t just the model organisms (although I do still love the mods, of course!). But cacao…mmmmm…..
But it is much more than just informative web pages. There are databases of collections including germplasm and species databases, geographically organized information, and more. There are training materials that faculty might want to use. There’s even a terrific collection of images of biodiversity that may be useful for presentations. Check out this brief (~3 min) introduction to the Bioversity International resources for more details.
That’s right, I got a couple of emails today and the International Society for Biocuration is open for membership! I unofficially joined right after I got home from the 3rd International Biocuration Conference where the society was introduced. I plan on paying my dues shortly after I get this post out, but since I don’t want to hog all the fun I wanted to blog about this oportunity ASAP.Here’s the text of the original announcement:
Dear Colleagues,
The International Society for Biocuration has redesigned the biocurator.org website, and we are happy to announce that member registration is now active. The member registration page is here: http://colleagues.biocurator.org/join
We strongly encourage people from the biocuration community to become members of the ISB. There are many goals we wish to achieve and that can only accomplished with the help and support from all of you (http://www.biocurator.org/mission.shtml). The membership rates for 2009-2010 are as follows:
Academia
Principal investigator: 60 CHF
Curator: 40 CHF Student: 20 CHF
Industry
Principal investigator: 120 CHF Curator: 80 CHF
Conversion rates for June 18, 2009:
1 CHF = 0.921 USD – 0.664 EUR – 0.563 GBP
Lydie, Pascale and Lorna
Seriously, I do believe with wide community support this society could really be valuable for curators and others associated with building and supporting bioinformatic resources. So please, help me spread the word!
My Tivo does not know me very well–I know it works for some people, but for some reason my Tivo thinks I speak Portuguese and that I like to cook. I wish I did, but I don’t. However, occasionally it gets it right. Last night as I was scrolling through the list I found an episode of Charlie Rose on Personal Genomics. It includes PGP (Personal Genome Project) participant Steven Pinker. Steven wrote a great article in the NYT on this after he got his genome done. George Church was on, who leads this project. And then Charlie talked with Linda Avey and Anne Wojcicki from 23 and Me.
I don’t think any of it was dramatically new to me, but if you aren’t familiar with the players in this topic and the issues at hand you might enjoy this episode. It is about 30min long. In case the embed doesn’t work here’s the URL: http://www.charlierose.com/view/interview/10399
The personal genomics discussion begins about 30min in to the full video. You can move the slider over to get to it right away.
I know sometimes I joke about “another day, another genome” as it seems like we can check off another genome daily. And as the next-gen technology spreads further that’s going to be even more common. It’s gotten me thinking a lot about which species ought to be done. And how will sequencing research teams choose?
The folks at the Agricultural Biodiversity Webloghave me intrigued on a bunch of resources that are not the ones that most bioinformatics folks in my sphere have focused on. I mean, I know why we focus so much effort on model organisms and the big food species like at Gramene and PlantGDB, and I support that. But when you start thinking about the other organisms that we rely on so much–in the big agriculture way and the small agriculture way–I think we need to bring those animals and plants into the herd And we can soon.
Their recent post Linking up livestock databases was the one that prompted this post. But they write a lot of things I like (especially about plant genetic resources) and really have me wondering and reading, and thinking about how to raise awareness on the other valuable species.
The livestock post pointed to several nice resources that I was unaware of before. In an article by Eildert Groeneveld in the Globaldiv Newsletter the focus in animals, and he offers several nice links. Check out the diverse sheep at the Heritage Sheep Breedsweb site. Check out the species in the Central Documentation for Animal Biological Diversity in Germanyhere. Or the breed data collection at Oklahoma State–have you ever seen goats like those Alti Mountain goats? Wowsa. How about the Domestic Animal Diversity Information System or DAD-IS? There are other great links as well in the newsletter–check ‘em out. Another thrust of the article is linking up individual data with breed data via the EFABIS project as well to enhance the knowledge, and you can learn more about that in the newsletter.
Anyway, there are some really fascinating variations here. Understanding them would be a great project for folks with a next-gen sequencer waiting for input. Have a look. And celebrate rare breeds. We are going to need them in times of climate change.
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Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to ask questions on the use of genomics resources. Think of us as a virtual help desk. If you have a question about how to access a certain kind of data, or how to use a database, or what kind of resources there are for your particular research problem, just ask in the comments. OpenHelix staff will keep watch on the comment threads and answer those questions to the best of our knowledge. Additionally, we encourage readers to answer questions in the comments too. If you know the answer to another reader’s question, please chime in! The “WYP” thread will be posted every Thursday and remain at the top of the blog for 24 hours. Questions or problems asked on Thursday will be answered on Thursday to the best of our ability. You can leave questions on other days of the week, but the answer might not come that day.
And there’s an important issue of 
