Tag Archives: Nature

Instruction precedes innovation

OpenHelix is founded on the premise and Mary made the point again recently on a guest post on Nature Blogs: SciVee – Making Science Visible.

Do you RTFM? C’mon—tell the truth. When you approach some new software, do you read the freakin’ manual first? Yeah. Thought so. Not to worry, it’s a common phenotype. In fact, we’re pretty sure that the scientists at OpenHelix are among a tiny fraction of people with a rare allele for software manual reading. But the good news is we’ve found a way to help non-rare allele people.

(RTFM… “Read the ‘forlorn’ manual” … F being something else… this is a family-friendly blog after all).

We absolutely know that a hour or a few of some structured training and learning about a biological database or analysis tool will save a researcher days, sometimes months, of work. Sometimes it will mean the difference between making an amazing discovery… or hitting a dead end.

Well, it was nice to read today in a comment in Nature  (David Piston, p440, behind a subscription wall) a perfect example of something we are evangelists about:

As head of Vanderbilt University’s core microscopy labs, I recently met a colleague and his student to discuss their confusing results from an experiment studying protein interactions in cells. After applying a treatment that should have disrupted the interaction of two particular proteins inside mitochondria, they still saw the proteins interacting. The student said that to measure the interaction he had used a commercial automated image- analysis system. He didn’t understand how it worked, so he just used a colleague’s settings from a different experiment. But, without him realizing, this had masked all of the cell except for the mitochondria. If he had

modified the settings to leave the entire cell unmasked, he would have seen that the proteins were now present within the mitochondria in relatively small amounts compared with the rest of the cell, and so their interaction had been disrupted — the treatment was, in fact, working.

In this case, it wasn’t inspiration that was lacking — it was instruction.

 He goes on to discuss how automation in research has been a boon, yet at the same time a bane.
It’s made it easier to get research done. This is going to sound like a ‘up the hill both ways… in the snow’ story, but a short (yes, I say.. short) 20 years ago when I started sequencing retrotransposable elements in drosophila, I used the Sanger method and used to fill lanes and lanes of  polyacrylimide gels. A few thousand base pairs of sequence took a long time, as in days (or weeks when I made a stupid mistake and cracked the huge glass set up our brilliant lab technician set up). Today, it’s automated and fast, blazing fast. As in hundreds of millions of base pairs in the same amount of time.
But, as Dr. Piston explains in the comment, this leads to researchers not understanding fully how the tool works and the parameters best to use:
they waste time by using a tech- nique improperly or, equally tragically, miss something exciting when they assume that a strange result means that they did something wrong and they never follow it up.
He speaks mainly to experimental tools at the bench and the need for more education and instruction. But it goes doubly so for databases and computational analysis tools, databases and tools that pretty much any and all biological researchers now need to access and use regularly… or should.
We have so many of our own anecdotes along these lines. There was the researcher in mycology who, when we showed them a couple databases of mycological information, were ecstatic. My best anecdote was a prominent researcher (won’t say who, when or where :D) who took a workshop with us on the UCSC Genome and Table browsers. This researcher came up to me afterwards and showed me the research being done in the lab and the month they had spent in a dead end trying to analyze the data. At the end of the workshop, they figured out their answer and told us that the 4 hour course probably just saved them 6 months of work.

We have a lot of anecdotes like that.

Read the comment, Dr. Piston has some very valid and important points and suggestions.

Oh, and… here comes the totally shameless plug…  you could always go watch our sponsored open access tutorials and do the exercises on UCSC Genome and Table browsers, ENCODE, PDB and others. Or our other 100 tutorials (subscription). Or one of our nearly 200 weekly tips (open access).

And we will be having a series of webinars in the next half year, the first to be announced in just about a day. So keep watch here.

Remember, instruction comes before innovation. You could save months of work… or even better, make a discovery that you’d never have made otherwise.

Piston, D. (2012). Research tools: Understand how it works Nature, 484 (7395), 440-441 DOI: 10.1038/484440a

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…

  • RT @32nm: ISCB Public Policy Statement on Open Access to Scientific and Technical Research Literature — Bioinformatics http://ff.im/x9hQ2 Hat tip to Mitsuteru Nakao [Mary]
  • The beginning of population level structural variation information on the human genome, from the at the  1000 genomes project. Hat tip to GenomeWeb [Jennifer]
  • Registration for the March 2011 GMOD Meeting is now open. See the wiki page at March 2011 Community Meeting. [Mary]
  • Need to assemble and analyze large datasets for multigene phylogenetic analysis? Might want to try out the new iPhy. Paper here. [Trey]
  • Ok, I had to go look at this–not what I expected…. : Top 200 Genomic Females list for Feb. 2011 is NOW ONLINE at http://bit.ly/i0Nj3O via @holstein_world. Yes, the name did clue me in, but I still had to look. [Mary]
  • Scientific Reports: interesting new venture by Nature Publishing Group. [Jennifer]
  • I love when rare diseases can shine lights into the darkness–very neat story on arterial calcification. Fascinating: RT @NatureNews: Solution to medical mystery offers treatment hope http://ff.im/-xiZYE [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…

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…

"Genomic Data Resources: Challenges and Promises" Published in Nature Education

Authors Warren Lathe, Donna Karolchik and other members of OpenHelix give an introduction to online, publicly available genomics resources at www.nature.com/scitable.

Seattle, WA (PRWEB) February 11, 2009 — OpenHelix today announced the publishing of an article introducing and exploring the many online genomics resources available to the public. With over 3,000 genomic resources, tools and databases available on the web, and more being added rapidly, the article also explores the various issues concerning the growth of these tools, their number, and the sheer size of the data available.

The article is published by Nature Publishing Group’s Nature Education division on their new Scitable portal. Scitable is an open online teaching and learning portal that publishes high-quality educational articles and combines community features to fuel the exchanges of scientific insights, teaching practices and study resources.

The success of future medical research is directly reliant on researchers being able to find and use the overwhelming genomics data now present and becoming available on the web
In this article we give a stepping-in point for those seeking to better understand the data and the resources used to present it to the scientific community.

“The success of future medical research is directly reliant on researchers being able to find and use the overwhelming genomics data now present and becoming available on the web,” explained lead author Warren Lathe, Chief Scientific Officer at OpenHelix. “In this article we give a stepping-in point for those seeking to better understand the data and the resources used to present it to the scientific community.”

Additionally, readers can find out more about these resources and access online tutorials, exercises, slides, Quick reference Cards and other training materials at www.openhelix.com. Many tutorials are sponsored by the resource providers themselves and are therefore free to the user. Over 60 tutorials are also available through a cost-effective subscription to individuals, groups or institutions.

Article Reference and Link:
LATHE, W., WILLIAMS, J., MANGAN, M., and KAROLCHIK, D. Genomic Data Resources: Challenges and Promises. Nature Education 1(3), (2008)

About OpenHelix:
OpenHelix, LLC, (www.openhelix.com) provides the genomics knowledge you need when you need it. OpenHelix provides online self-run tutorials and on-site training for institutions and companies on the most powerful and popular free, web based, publicly accessible bioinformatics resources. In addition, OpenHelix is contracted by resource providers to provide comprehensive, long-term training and outreach programs.

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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Metagenomes in Nature

Nature had a nice feature on metagenomics last week and another on the Human microbiome metagenomics. You’ll need to have a subscription to access those :(, but the gist of the latter news feature is the possibilities of Human microbiome research, pros and cons and the projects out there. There are a lot. In order of amount of funding they are:

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