Tag Archives: research

Friday SNPpets

Welcome to our Friday feature link dump: 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…

  • A bit of a dust-up at ScienceBlogs as they added a corporate blog (Pepsi writing about nutrition science) and several of the bloggers left or threatened to leave. The Pepsi blog is no more. I hope that’s resolved, ScienceBlogs is an excellent collection of science writing. [Trey]
  • Pathway Tools Workshop 2010 held by the folks from BioCyc announced for October 21-25: http://bioinformatics.ai.sri.com/ptools10/ [Mary]
  • Animal portraiture against a white background. It’s been done before, this time with birds. It always reminds me how amazingly beautiful life can be. [Trey]
  • VectorBase announces that they have moved to the new style Ensembl browser with their current release–Yeah!  If you are interested in “Invertebrate Vectors of Human Pathogens”, this database may have species you want to know about. [Mary]
  • A good discussion about the recent ‘longevity gene’ study and it’s possible flaws by Razib Khan of Gene Expression [Trey]
  • Bandwidth-heavy, but really neat movies of tumor angiogenesis. You can open the Navigator menu to see the various movies listed, or you can migrate around the tumor yourself.  Hat tip to Jill!  [Mary]
  • On the GBrowse mailing list people were looking for examples of GBrowse 2.0 in action. WormBase indicated they are up to that version, and there was another research group with a species I never heard of before that also has it running: Gardnerella vaginalis.  They have compared 2 strains: one from a healthy woman, one suffering from infection. They show divergence, interestingly.  You can check out their recent publication on it from their publication tab.  A nice demonstration of how to use GBrowse for your species of interest. [Mary]

Librarians and Science, discuss

A discussion well worth having. Dorothea Salo at “The Book of Trogool’s” recent post on Science Online 2010 (which one of us attended) mentions an interesting exchange she (a librarian) had:

Interlocutor: “So what do you do?
Me: “I’m a librarian.”
Interlocutor: *lengthy pause* So… what are you doing here exactly?

Er, what? A conference about science communication? How on earth can that not be imagined to intrigue a librarian?

This, ladies and gentlemen. THIS. Right here. This disconnect is the number-one threat to science librarianship today—perhaps to all academic librarianship. How can science libraries persist when scientists haven’t the least notion that libraries or librarians are relevant to their work?

I noticed a similar discussion going at STELLA (manifested in topics on embedding, the library of the future and science 2.0). My basic take on this is that researchers are are going to need physical libraries less and less (do they really need them now?) and librarians more and more (but they don’t seem to realize that). I commented as such on the post above.

Deepak Singh has asked a similar question today, and started a discussion.

Impact Factor

I remember considering the “Impact Factor” of journals when submitting research papers, and wondering what the impact factor of a specific paper I published might be out of curiosity. Not particularly seriously, my field was narrow enough in my Ph.D. research that there were just a few journals to even consider, so it was usually pretty simple choosing. And for individual articles, I am pretty sure I knew the 4 people in the world outside my lab that were interested in my research (I jest, a little). During my postdoc, my PI was pretty good and choosing journals based on the article, the journal’s audience… and impact factor.

But impact factor measuring has it’s issues (Article-Level Metrics and the Evolution of Scientific Impact, Neylon and Wu. PLoS Biol 7: e1000242), and there is always a search to measure the impact of journals and individual articles better, or at least differently. Well, one of my favorite science sites and one of my favorite journal publishers ResearchBlogging.org and PLoS, have worked together to measure the impact of journal articles. PLoS has a lot of metrics to see what the ‘impact’ of an article might be, and now they’ve added a metric to see how many times it’s been written about on blogs using blog aggregators like Postgenomic, Blog Lines and Nature Blogs, and now ResearchBlogging.

I like the partnership with ResearchBlogging specifically because whereas the other blog aggregators are not necessarily picking up articles that discuss the science of the article (Postgenomic) or aggregate only a subset of science blogs out there (Nature Blogs), ResearchBlogging is specifically blogs posts discussing the research of  peer-reviewed articles.

Of course I don’t find this particularly useful to compare one article against another (the best articles aren’t always written about, and those that are might not be in the blog aggregators), but I do think this will be great way to carry on the conversation and dig deeper into the research topic.

You can view that metric at PLoS of any article, for example the one I link to above, click on the “metric” tab, scroll down a bit until you see the heading “Blog Coverage.” For that article, you’ll see two ResearchBlogging posts (as of this writing), a metric for this paper about metrics :).

iPhone and research

Ok, so I just got my new iPhone 3Gs. I couldn’t resist. Anyway, my contract on my first generation iPhone was up. So, it was time to reconfigure and explore the huge number of apps out there for the iPhone.

I use the iPhone for a lot of things, directions, finding out what stores are in the area, keeping my grocery list, listening to music, watching shows, browsing the web, keeping my calendar and contacts and a bunch more. Oh, and to make and receive phone calls :).

I’ve read past posts on other blogs about scientific apps for the iphone, I decided it was time to check out what apps there are now.

I’ve found a few I like, some that might work (I do computational genomics now, so I haven’t tried the ones for the bench), and one that has nothing to do with biology (directly anyway), but I am in love with. Follow me below the fold.

Continue reading

What's your problem? Open Thread

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to askq_mark2.jpg 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.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.

What's your problem? Open Thread

q_mark2.jpgWelcome 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.

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.

What's Your Problem? Open Thread

Welcome to the “What’s Your Problem?” (WYP) open thread. The purpose of this entry is to allow the community to askq_mark2.jpg 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.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.

What’s Your Problem? Open Thread

q_mark2.jpgWelcome 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.

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’m closing comments here since a fresh thread is up–Mary}

What's your problem? Open Thread

q_mark2.jpgWelcome 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.

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.

What's Your Problem? Open Thread

q_mark2.jpgWelcome 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.

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.