Notebook Daniel S. Standage

Roundup of links from the last week's worth of interesting reads.

A couple of weeks ago, I saw a couple of Twitter threads explode on the topic of citing "manuscripts in progress" on one's CV.

OK I just saw an application that listed a prestigious journal name for a paper that is IN PREPARATION. Not even submitted. #stopthemadness

— Michael Hoffman (@michaelhoffman) February 8, 2016

Postdoc applicants - seriously, don't do this …

The NCBI Transcript Shotgun Assembly database is the go-to place for submitting transcript assemblies for long-term archival and public access. However, TSA is not one of the database options provided when doing keyword searches at NCBI. TSA sequences are available through the nuccore nucleotide database, along with all other DNA and RNA sequences.

If you want to search NCBI exclusively …

Roundup of links from the last week's worth of interesting reads.

Intervals are one of the most common data abstractions used in genome informatics, along with strings and graphs. DNA has an intricate dynamic three-dimensional structure, but for many bioinformatics applications we can get away with ignoring this level of detail and representing the molecule instead as a static linear sequence of symbols. Genomic features—such as genes or transposable elements …

I've been trying subtly (and in a few cases not-so-subtly) for years now to convert my colleagues to the gospel of git and GitHub. The git version control system has its quirks no doubt, but there is—in my opinion—no more powerful system for open collaboration on software and science than git and GitHub. A quote I attribute (hopefully …

Roundup of links from the last week's worth of interesting reads.

Some notes on my data forensics to determine whether there are any differences between the RefSeq Arabidopsis annotation and TAIR10.

Roundup of links from the last week's worth of interesting reads.

Walking through the process of converting my pen-and-paper sketch of a decision tree into a computer graphic with graphviz.