OPTIMising Genome Assembly This month brings new additions to our exciting and on-going Optical Mapping series. Outside of a handful of key genomes, due to deficiencies in the short sequencing read lengths that have backed genome assembly, we lack reference genomes that are finished to high standards that can support comprehensive analyses.

tl;dr: Data from thousands of non-retracted articles indicate that experiments published in higher-ranking journals are less reliable than those reported in ‘lesser’ journals. Vox health reporter Julia Belluz has recently covered the reliability of peer-review.

Over the last decade or two, there have been multiple accounts of how publishers have negotiated the impact factors of their journals with the “Institute for Scientific Information” (ISI), both before it was bought by Thomson Reuters and after. This is commonly done by negotiating the articles in the denominator.

tl;dr: It is a waste to spend more than the equivalent of US$100 in tax funds on a scholarly article. Collectively, the world’s public purse currently spends the equivalent of US$~10b every year on scholarly journal publishing. Dividing that by the roughly two million articles published annually, you arrive at an average cost per scholarly journal article of about US$5,000.

In a big step forward for allowing proper credit to be provided to all of the awesome folks collecting and publishing data, the journal Global Ecology & Biogeography has just announced that they will start supporting an unlimited set of references to datasets used in a paper. These references will be included immediately following the traditional references section in both the html and pdf versions of the paper.

In Germany, the constitution guarantees academic freedom in article 5 as a basic civil right. The main German funder, the German Research Foundation (DFG), routinely points to this article of the German constitution when someone suggests they should follow the lead of NIH, Wellcome et al. with regard to mandates requiring open access (OA) to publications arising from research activities they fund.

Last Christmas we gave you our heart; okay forget George Michael – we gave you beautiful imaging data sets, Virtual Machines, BYO data parties, GigaGitHub, more open peer review plus much more.

Despite the precipitous drop in the price of DNA sequencing, global credit crunches have tightened the science budgets able to properly take advantage of the potential of genomics. While this plummet in cost has led to an explosion of “mega-sequencing” projects carried out by large international consortia, it has also democratized and empowered what can be done outside traditional academia and research funding environments.

Posting my reply to a review of our most recent grant proposal has sparked an online discussion both on Twitter and on Drugmonkey’s blog. The main direction the discussion took was what level of expertise to expect from the reviewers deciding over your grant proposal. This, of course, is highly dependent on the procedure by which the funding agency chooses the reviewers.

Update, Dec. 4, 2015: With the online discussion moving towards grantsmanship and the decision of what level of expertise to expect from a reviewer, I have written down some thoughts on this angle of the discussion. With more and more evaluations, assessments and quality control, the peer-review burden has skyrocketed in recent years.