Evaluating Trends in Bioinformatics Software Packages

Genomics — the study of the genome — requires processing and analysis of large-scale datasets. For example, to identify genes that increase our susceptibility to a particular disease, scientists can read many genomes of individuals with and without this disease and try to compare differences among genomes. After running human samples on DNA sequencers, scientists need to work with overwhelming datasets.

Working with genomic datasets requires knowledge of a myriad of bioinformatic software packages. Because of rapid development of bioinformatic tools, it can be difficult to decide which software packages to use. For example, there are at least 18 software packages to align short unspliced DNA reads to a reference genome. Of course, scientists make this choice routinely and their collective knowledge is embedded in the literature.

To this end, I have been using ContentMine to find trends in bioinformatic tools. This blog post outlines my approach and demonstrates important challenges to address. Much of my current efforts are in obtaining as comprehensive a set of articles as possible, ensuring correct counting/matching methods for bioinformatic packages, and making this pipeline reproducible.

Peter talks about ContentMine and WikiData at Wikimania

8/8/2014

 

ContentMine and WikiData from petermurrayrust

Open science Rio (OSRio) Peter talks about Open Data and Open Notebook Science

12/8/2014

Picture courtesy of Alessandra Bax @alessbx and Leslie Chan @lesliekwchan

 

Open data and Open Science from petermurrayrust

Ross Mounce talks about Open Scholarship at King’s College, London

4/9/2014

 

Open scholarship [a FOSTER open science talk] from Ross Mounce

Wiley’s “Free to read” actually means “pay 35 USD”

Posted on December 16, 2014 by pm286

I got the above unwanted Twitter from Wiley (I have checked as far as possible that it’s genuine). It seems to be Wiley advertising a free to read article. I have pasted the message so you can try this at home:

Progress in #nanotechnology within the last several decades review from @unifr is #freetoread! http://ow.ly/FXDFQ

I check the poster https://twitter.com/ChemEurJ/status/544832871564050432/photo/1 and it seems to be a genuine site. So off I go to get my free copy (sorry, my free set of photons for sighted readers)…

 

I click the “View Full Article (HTML)” and get…

So Wiley equate “35 USD” with “free to read”.

I don’t.

I’m sure it’s a BUMP-ON-THE-ROAD (Elsevier excuse).

But this is the independent fourth publisher foul-up I have got in the last four days. We pay them 20 Billion USD and they can’t get it right.

Elsevier’s Bumpy Road; Unacceptable licence metadata on “Open Access”

Posted on December 12, 2014 by pm286

I am looking for Open Access articles to mine and since I have recently become an astrophysicist I started with http://www.sciencedirect.com/science/article/pii/S1384107614000426

Can I mine it?

“Open Access” means virtually nothing. Let’s try RightsLink, the tax-collector for the toll-access scholarly publishers. Normally a depressing experience, but here’s a surprise.

Rightslink can’t work out the licence.

(PMR can’t work out the licence either). Sometimes it hides at the bottom of the document…

PMR still can’t work it out? Is it Open.

The only certain thing is that even after years of mislabelling documents Elsevier is still incapable of reliably attaching licence information to document.

I ASSUME THE AUTHORS HAVE PAID THOUSANDS OF DOLLARS FOR THIS.  THEY DESERVE DECENT SERVICE. I AM ANGRY.

UNIVERSITIES AND FUNDERS, YOU’VE PAID FOR THIS ,  AREN’T YOU ANGRY?