Tag Archives: ScienceOnline

Friday SNPpets

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…

  • Snorf. RT @szintri: “underappreciated fact of genome assembly…the choice of assemblers is often limited to those that run without crashing” via @JChrisPires [Mary]
  • RT @yokofakun: the correct URL for VARMD is http://t.co/AvNWueQU  “analyzing the DNA sequence variants produced by human exome sequencing” [Mary]
  • Found this GenomeWeb article interesting – Lot to think about/figure out: “White House Bioethics Commission Tackles Genomic Data” [Jennifer]
  • RT @drbachinsky: Personal genomes hold eventual promise for treatments – Mass High Tech Business News http://t.co/PQFqqbPf [Mary]
  • I’m working on my ScienceOnline2012 report(s), but in the meantime check out this list of blog and media coverage from before, during and after the conference here. [Jennifer]
  • Don’t forget to register & attend our free ‘How to use the RSCB Protein Data Bank’ Webinar, sponsored by the RCSB PDB. The webinar is based on our newly update, full length tutorial and will be presented next Wed. at 2 pm ET. You can register on the OpenHelix webinar page. [Jennifer]
  • RT @JChrisPires: X Prize: Build a Star Trek ‘tricorder’ and win $10m http://t.co/Vt8L63Ub via #science #technology #SciFi #Startrek #genome #bioinformatics [Mary]
  • RT @drgitlin: Will Gene Patents Derail the Next-Generation of Genetic Technologies?:  A Reassessment of the Evidence Suggests Not http://t.co/QdeiwmEp [Mary]
  • RT @m_m_campbell: A healthy marriage. Bringing human #genetics & functional #genomics together to improve #health. Great read http://t.co/AR0XZsXu @NatureNews [Mary]

Friday SNPpets

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…

Tip of the week: ResearchBlogging and PubGet

A couple of years back the OpenHelix team attended the first ScienceOnline science blogging conference (and the subsequent ones too).  The repercussions of this continue to affect what we do today. We got tips on effective blogging, we got leads on great tools, and we became part of the science blogging community–a chatty and helpful network of people who really want to communicate science more broadly and effectively.

One of the tools we learned about back then we continue to use regularly is ResearchBlogging.  I thought today I’d introduce this utility because we’ve found ourselves in conversations with people who would like to have some kind of mechanism to discuss research in their fields, but weren’t aware of this opportunity.

The short story: ResearchBlogging is a blog post aggregator (and more). If you blog on peer-reviewed research papers, you can obtain a little bit of code from the ResearchBlogging citation generator.  You register your blog, and use this code, the RSS feed sweep from ResearchBlogging detects your post and brings it over to the main site.  It also distributes it to other sites that host the widget with recent posts.  If you hang out at ScienceBlogs you’ve probably seen the widget on the right when reading blogs over there.  ResearchBlogging also automatically tweets your entry via Twitter.  Every time we use this, we see increased traffic from both the main site, from the widget, and from Twitter.

The longer story: ResearchBlogging is a community of science communicators.  Some of them are in your field, some are in far dispersed fields.  But they want to talk science.  They offer substantive discussion on papers they’ve read. Sometimes this is praise for the work, sometimes not.  Sometimes it opens the discussion to new ideas. Sometimes it is a launching point for further discussion in other directions.  The posts vary, of course.  Sometimes they are like having a discussion around the water cooler about some paper a colleague read.  Other times they are more like a journal club.  There are guidelines that describe the goals in more detail, and there is a community forum for discussions about it.  There’s also an editor’s selection: if your post is selected by the editors for the quality, even more people will see your work.  They also recently held a competition for quality in science blogging, and recognized many science bloggers who are taking science out of the journals and on to the web.

We use this often to discuss new software papers we’ve seen.  As great as papers are, especially for software we find we want to give a bit of a movie about the software and how it is used–so for us the paper is usually a launching point for a software tip.

Recently ResearchBlogging has also teamed with the PubGet folks.  PubGet is a cool type of literature search that can be integrated into your local journal subscription set, and it’s a speedy way to get access to PDFs you might want.  But the bonus piece is that if a paper in PubGet has been blogged in the ResearchBlogging system, a little icon indicates this.  So you can go look at what the science blogger had to say about that paper as well.

So for this week’s tip of the week I demonstrate the mechanics of how to get that bit of code from ResearchBlogging, using the DOI or digital object identifier, where to put it back on your blog, and then show how PubGet can lead you to cool discussions of papers that you might be interested in.

For more details:

ResearchBlogging help: http://researchblogging.org/static/index/page/help

ResearchBlogging guidelines: http://researchblogging.org/news/?p=53

PubGet: http://pubget.com/

OpenHelix page of stuff we’ve done with ResearchBlogging: http://researchblogging.org/blog/home/id/154

ScienceOnline2010: Making Connections

ScienceOnline2010 occurred just over two months ago now, so this post is slow in coming, but I think you’ll understand after I explain. You see, really good conferences are often so intense and so full of new ideas that it can take some time before you can fully cull, and then express your thoughts. That’s what I’ve been doing for the last few months – chewing on ideas of connections – well, that and doing my ‘real’ work, which is making our tutorials.

I think I need to first describe where my idea comes from, before I tell you my idea. At ScienceOnline I didn’t really have any set agenda of what sessions I wanted to go to. I just went and absorbed and discussed wherever whim took me. I ended up in sessions about Math, science reporting, librarians, Martin Luther King Jr., legal issues of blogs, government 2.0 and more. The librarian session was an interesting look into the new age of what digital librarians can offer researchers and others. It was co-chaired by Dorothea Salo and Stephanie Willen Brown, and Trey has linked to a post by Dorothea on the same subject. The MLK session dealt with mechanisms for engaging underrepresented groups in online science media and was chaired by David Kroll and Damond Nollan. In that session someone mentioned that they had difficulties in having enough applicants for opportunities reserved for students from underrepresented groups & discussion followed as how to best notify such students of the opportunities. At approximately the same time I had been hearing about abundant STEM funding, and from a friend about her efforts to secure funding for after school workshops at a community library that largely served underrepresented groups.

I truly enjoy finding possible connections among groups that might solve a problem – to me it is like a mental puzzle that I find addictive. The idea that I came up with is for librarians at universities to collaborate with community librarians to provide STEM programs to encourage students in target populations to learn about, and enjoy, and be prepared for opportunities in science that might be available to them. In my way of thinking, it would provide university librarians a new service that they could provide their institutions with (i.e. outreach to underrepresented groups of students). It would provide a possible support system (financial, physical, collaborative and more) to community librarians trying so hard to support their communities in so many ways (after school programs, tutoring, mentoring, job placement – the list of what is needed from a community library goes on and on), often with little support. It would be of value to the universities because they gain an in road to the populations that they wish to reach. And if it does work it would be of value to our nation because it would help reduce racial barriers and lead to a better, more productive economy. I emailed a few people in the MLK session about my idea, but didn’t really follow through – I figured it might be just another of my silly/optimistic/foolish ideas.

Well, a week or two ago I happened to mention my idea to the friend with connections to a community library – actually to a librarian who was trying to find some sort of funding mechanism for her after school programs after her library was closed due to city budget issues. My friend fell sort of quiet, which I took as more evidence that the idea was off. Today she emailed & it turned out the silence was listening & some idea-chewing of her own. She went to a small local college with her workshop idea, and they were so excited about the concept that they have signed on to sponsor her summer workshop. The details aren’t all worked out, but it is enough encouragement for me to get the confidence to go public with my idea & ask if you think it would work on a larger-scale. Librarians, is your university likely to find value in such an effort? Educators, how could you envision adding your efforts to STEM education projects? Community members, do you see any value/interest in these ideas? What are your ideas for bridging gaps and helping to solve these issues? Any creative comments or follow-on ideas are much appreciated, as are reports of successful (or even attempted) implementations of similar efforts/ideas.

The Deadline is This Friday for the Biocuration Conference!

biocurator_berlin_logoI just got an email that the registration for the 3rd International Biocuration Conference closes this Friday, March 27th. The conference is April 16th-20th in Berlin and if there is ANY way you can get there, I suggest you do! It is a GREAT meeting – I’ve had the pleasure of attending both the 1st & 2nd meetings in the past, and will be representing OpenHelix at this one too. This meeting is a really cool, small meeting where resource creators and curators come together to exchange ideas and discuss solutions to current and future bioinformatics problems. I really hope that some of the bloggers I met at ScienceOnline in January make it to this meeting – I think the two groups have a lot in common. It is also a great place to hear about new resources. OpenHelix (ok, I) will be introducing a new resource in fact. Mary alluded to it in her comment reply to Theadore. If you are going to be in Berlin with me, you can stop by poster F12 on Friday night 4/17 19:00-22:00, or come to my talk during the Sunday morning session 4/20 8:30-10:00 to hear more!

A bit more on ScienceOnline09

science_online_09_logo.jpg I’m still culling my memories & scribbled notes from ScienceOnline09 (moving a little slow here, but coffee just isn’t helping yet – maybe I should try sleep…)  OK, um, oh yea - if you want to see what I got into before I get a full blog post out, check out the Conference Program. It has all the sessions described & many have links to discussions, other resources, free stuff, etc. It is actually a really deep resource in & of itself!

…And Boy is My Brain Tired…

You know the old joke “I just flew in from X, and boy are my arms tired!”? Well I didn’t fly, I drove, and its my brain not my arms, but that’s the way I feel this Monday morning.

 I spent my weekend with an amazing group of science communicators discussing a vast range of topics and issues. I attended a Women In Science & Engineering (WiSE) event Friday evening, and participated in the ScienceOnline09 unconference Saturday and Sunday. For those of you who are wondering what an ‘unconference’ is, it is where every session is a discussion that has a leader or two. The leader is sort of like a guide – lays out an issue, guides the discussion but is not allowed to monopolize the discussion time & audience participation is mandatory. For a hermit like me who works alone in a quiet office all day, it was a bit overwhelming – so many discussions, ideas, new things to learn about, topics to think about – there were so many excellent exchanges between so many enthusiastic people, just the volume of sound in the conference hall could be overwhelming at times.

 I will  definitely be blogging more of the details (as I can get them organized in my brain – might require more coffee…) but here I wanted to specifically say thanks to all who were involved, and to let all of the sponsors know that this was an excellent conference and well worth your support! Thank you very much, and please continue your support in the future!

Data and how to handle it – biocuration and beyond

female_computer_idea.jpgI was enjoying a wonderfully wet, gray autumn day – you know the kind – just perfect for curling up and reading a good book with a hot cup of tea. I figured I’d just indulge in a little break from writing & revising drafts of tutorials and publications. I was going to allow myself one Nature article – “The future of biocuration“, which I’ve been meaning to read since it came. The article was written by several biocurators and describes the exponential growth in the amount of available biological data and proposes three urgent actions:

1. collaboration among authors, journals and curators to expedite the exchange of data between databases and journal publications

2. development of a recognition structure that encourages community curation

3. establishment of scientific curation as an accepted professional career

computer_information.jpgThe article makes a lot of good points, and I highly recommend you read it if you are interested in the future of databases at all. But as I began reading, I couldn’t stop. The special feature of this whole issue of Nature is ‘Big Data: Science in the petabyte era’. I really think Nature did a great job of finding and presenting many many points of view on the subject of big data – some that I’ve been thinking about as I register for upcoming meetings – and some I’ve never considered, but can now see how they make so much sense…

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