Shannon Stream of Consciousness…

Posted on 6 CommentsPosted in Bioinformatics, Publishing, software

A new transcriptome assembler has been released. Shanon: and It looks quite interesting from an algorithm standpoint and claims to be better than the existing suite of assemblers.. Good deal, I\’m all ears! I\’ll hope to provide a full review (with the lab) in a bit, but I have a few immediate suggestion after kicking […]

Feeding your Transcriptome with the Oyster River Protocol

Posted on Leave a commentPosted in Bioinformatics, Publishing

After months of work,  my new manuscript \”An opinionated guide to the proper care and feeding of your transcriptome\” is out on bioRxiv!! Accompanying this is a living document – the version controlled and updated set of current best-practices \”Oyster River Protocol for Transcriptome Assembly\”. These documents serve to provide evidence-based guidelines for de novo […]

I will never understand

Posted on Leave a commentPosted in Publishing

begin{rant} I will never understand why it takes bioRxiv so many hours to \’screen\’ a preprint. Here are some solutions. Ask for volunteer screeners. These are people that have already submitted preprints to bioRxiv in the past, and therefore are \’trustworthy\’. As I\’ve said in the past – I\’d volunteer. Even if people screened a […]

On the quantity of methods sections

Posted on 7 CommentsPosted in Bioinformatics, Publishing

So last night I discovered an extremely interesting paper, \’The First Myriapod Genome Sequence Reveals Conservative Arthropod Gene Content and Genome Organisation in the Centipede Strigamia maritima\’ by Richards and colleagues. After reading the abstract, for genomics papers I always read the methods sections next. I like to know how the authors did what they […]

Transcriptome Assembly: A reviewers guide

Posted on 4 CommentsPosted in Bioinformatics, Publishing

I am writing this, in hopes that it will remind people (reviewers) of the critical details required of published transcriptome studies. This guide intends to cover the details through the production of the final transcriptome assembly. I will write about testing for differential expression at a later date. The ‘living document’ available for editing is […]

Go home GScholar, you’re Drunk!

Posted on 1 CommentPosted in Publishing

I was looking at the Assemblathon2  paper in Google Scholar, lamenting the fact that it is still not properly indexed when I got to noticing something funny- the number of citations the paper has received varies depending on whose page you are looking at. 3 different pages, 3 different numbers of cites.. I wonder which […]

PeerJ Preprint server for ALL of Biology!

Posted on 2 CommentsPosted in Publishing

I just got done uploading a manuscript to the PeerJ Preprint server.  It was awesome! This was a manuscript that was outside even the loosest of definitions of quantitative biology, and therefore not appropriate for arXiv. I am really keen to see biologists using preprint servers, and up until now, where to send non quant. manuscripts was a […]