Thread count in HMMER3

It's come to my attention (one helpful email, plus some snarky subtweets) that the --cpu flag of HMMER3 search programs may have a bad interaction with some cluster management software.

The --cpu n argument is documented as the "number of parallel CPU workers to use for multithreads". Typically, you want …




snoscan and squid in the 21st century

Back in the 20th century, when Todd Lowe was a happy PhD student in my lab in St. Louis instead of toiling in irons as professor and chair at the Department of Biomolecular Engineering at UCSC, he wrote a program called snoscan for searching the yeast genome sequence for 2'-O-methyl …




Go sign this.

Imagine you're a legal US resident, with a legal position in the US. You're away visiting your family in another country, and when you try to fly back home to the US, the US government won't let you back in. You could be a PhD student or a postdoc in …




Open position: Bioinformatics scientist

Michele Clamp is building up Harvard's bioinformatics team on the college (Cambridge) campus, and she's got an open position in collaboration with Susan Mango's group:

The Mango Lab in the Harvard Department of Molecular and Cellular Biology in collaboration with the FAS Informatics Group seek a bioinformatician for genomics analysis …




New open positions

We have two new open positions in the group. We are looking for a bioinformatics analyst and a scientific software engineer to join the teams that develop the HMMER and Infernalsoftware packages for biological sequence analysis. The teams are growing, with a key new team member Nick Carter, who …




from zero to python

Students actually showed up, so we really do have to teach the course. MCB112 Biological Data Analysis is now in its first week.

The tricksiest bit in the first couple weeks is bringing people up to speed in writing Python, for people who've never written code before. We trust in …




open position: lab coordinator

We have an open position for a new lab coordinator. Ads are running at Nature and elsewhere. Our LC is our point of contact for everything administrative that makes the lab run smoothly, including responsibility for our financial accounting/purchasing with both HHMI's and Harvard's systems, tracking our funding, managing …




Biological Data Analysis

I'm starting to plan a new Harvard course that'll be called Biological Data Analysis. Biology is going through a culture change. It's suddenly become a data-rich, computational analysis-heavy science. Are we going to outsource data analysis to bioinformaticians and data science specialists, or are biologists going to analyze their own …




Open software/web engineer positions

The lab's growing - the new space opened in November - and we're starting to get settled in. Now we're looking for a scientific software engineer and a web portal engineer to join the group.

The scientific software engineer will play key roles in the HMMER and Infernal projects, including optimization, parallelization …




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