Instructor training at the 2017 Data Intensive Biology Summer Institute at UC Davis

[Adapted from Titus Brown’s blog post]

Titus Brown has been so kind as to invite me to co-instruct this week-long workshop (thanks!). So I thought to make a bit of a commercial for it:

Are you interested in

• Getting started with, or getting better at, teaching the Analysis of High Throughput Sequencing Data
• Hands-on training in good pedagogical practice
• Becoming a certified Software/Data Carpentry instructor
• Learning how to repurpose and remix online training materials for your own needs

… then this one-week workshop is for you!

When: June 18-June 25, 2017 (likely we’ll only use Monday-Friday).
Where: University of California, Davis, USA
Instructors: Karen Word, C. Titus Brown, and Lex Nederbragt

This workshop is intended for people interested in teaching, reusing
and repurposing the Software Carpentry, Data Carpentry, or Analyzing High Throughput Sequencing Data materials. We envision this course being most useful to current teaching-intensive faculty, future teachers and trainers, and core facilities that are developing training materials.

Attendees will learn about and gain practice implementing evidence-based teaching practices. Common pitfalls specific to novice-level instruction and bioinformatics in particular will be discussed, along with associated troubleshooting strategies. Content used in prior ANGUS workshops on Analyzing High Throughput Sequencing Data will be used for all practice instruction, and experienced instructors will be on hand to address questions about implementation.

Attendees of this workshop may opt to remain at the following ANGUS two-week workshops so that they can gain hands-on experience in preparing and teaching a lesson.

This week-long training will also serve as Software/Data Carpentry Instructor Training.

Attendees should have significant familiarity with molecular biology and basic experience with the command line.

We anticipate a class size of approximately 25, with 3-6 instructors.

The official course website is here.

Apply here!

Applications will close March 17th.

The course fee will be $350 for this workshop. On campus housing may not be available for this workshop, but if it is, room and board will be approximately $500/wk additional (see venue information). (Alternatives will include local hotels and Airbnb.)

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If you have questions, please contact dibsi.training@gmail.com.

How to sequence and assemble a large eukaryote genome with long reads in 2015

I get asked about this a lot, so I thought to put together a quick blog post on it.

Disclaimer: this is the advice I usually give people and is given without warranty. As they say, Your Mileage May Vary.

Main advice: bite the bullet and get the budget to get 100x coverage in long PacBio reads. 50-60x is really the minimum. Detailed advice:

Sequencing and assembly

• get 100x PacBio latest chemistry aiming for longest reads (make sure provider has SAGE Blupippin or something similar)
• get 100x HiSeq paired end regular insert
• run PBcR on the PacBio reads, this is part of Celera. It corrects the longest raw reads, assembles them using Celera (long run time). Make sure to install the latest Celera release which uses the much faster MHAP approach for the correction.
• alternative is FALCON https://github.com/PacificBiosciences/FALCON
• run quiver for polishing the assembly using ALL raw PacBio reads, see tips here
• you could repeat the polishing if that changes a lot of bases and does not negatively impact validation
• polish using the HiSeq reads with Pilon

Optional:

• increase contiguity using BioNanoGenomics data
• create pseudo chromosomes using a linkage map (software?)

 

Notes from the ”FEBS-IUBMB workshop on education in molecular life sciences”

I attended the ”FEBS-IUBMB workshop on education in molecular life sciences”, 18 – 19 SEPT 2015, in Oslo, Norway. Although ‘molecular life sciences’ is part of the workshop title, many of what was discussed was applicable to a much wider range of subjects.

At the workshop, I presented a poster based on my recent blog post on “Active learning strategies for bioinformatics teaching” (the first time I turned a blog post of mine into a poster…). The poster can be viewed on FigShare. I managed to make the poster a bit interactive itself, by having a small quiz on it. The results speak for themselves:

A quiz to make a poster on active learning techniques interactive

Active learning strategies for bioinformatics teaching

The more I read about how active learning techniques improve student learning, the more I am inclined to try out such techniques in my own teaching and training.

I attended the third week of Titus Brown’s “NGS Analysis Workshop”. This third week entailed, as one of the participants put it, ‘the bleeding edge of bioinformatics analysis taught by Software Carpentry instructors’ and was a unique opportunity to both learn different analysis techniques, try out new instruction material, as well as experience different instructors and their way of teaching. On top of that the group was just fantastic to hang out with, and we played a lot of volleyball.

I demonstrated some of my teaching and was asked by one of the students for references for the different active learning approaches I used. Rather then just emailing her, I decided to put these in this blog post.

The motivation of turning to active learning techniques is nicely summarised in a post on the ‘communications of the ACM’ blog entitled “Be It Resolved: Teaching Statements Must Embrace Active Learning and Eschew Lecture”. I highly recommended reading it and checking out the references mentioned. I am by no means an expert in the area, and simply am learning by doing. I have no ways to measure whether the techniques I use are beneficial, but student responses strongly encourage me to keep applying them. My teaching is also very much influenced by my being a Software Carpentry instructor.

The following describes what I do in the de novo genome assembly module of the ‘High Throughput Sequencing technologies and bioinformatics analysis’ course I organise (link to materials). I used part of that module for the NGS Analysis Workshop (link).

A hybrid model for a High-Performance Computing infrastructure for bioinformatics

I work for the Norwegian High-Throughput Sequencing Centre (NSC), but at the Centre for Ecological and Evolutionary Synthesis (CEES). At CEES, numerous researchers run bioinformatic analyses, or other computation-heavy analyses, for their projects. With this post, I want to describe the infrastructure we use for calculations and storage, and the reason why we chose to set these up the way we did.

In general, when one needs high-performance compute (HPC) infrastructure, a (group of) researcher(s) can purchase these and locate them in or around the office, or use a cloud solution. Many, if not most, universities offer a computer cluster for their researchers’ analysis needs. We chose a hybrid model between the universitys HPC infrastructure and setting up one ourselves. In other words, our infrastructure is a mix of self-owned, and shared resources that we either apply for, or rent.

On graph-based representations of a (set of) genomes

In 1986, in a letter to the journal Nature, James Bruce Walsh and Jon Marks lamented that the upcoming human genome sequencing project “violates one of the most fundamental principles of modern biology: that species consist of variable populations of organisms”. They further wrote: “As molecular biologists generally ignore any variability within a population, the individual whose haploid [sic] genome will be chosen will provide the genetic benchmark against which deviants are determined”. They conclude that ” ‘the’ genome of ‘the’ human will be sequenced gel by acrylamide gel”.

We have come a long way when it comes to taking population variation into account in molecular/genetic/genomic studies. But these sentiments, expressed already in 1986, echo some of the trends in the human genetics field: the move away from a single, linear representation of ‘the’ human genome. In this post I will provide some background, explain the reasons for moving towards graph-based representations, and indicate some challenges associated with this development.

Thoughts on a possible Assemblathon3

The Genome10K meeting is ongoing (I am not attending but following through twitter). Today, there will be a talk by Ian Korf about the feasibility of an Assemblathon 3 contest (see this tweet and the schedule). Earlier the @Assemblathon twitter account asked for a wishlist for an Assemblathon 3 through the hashtag #A3wishlist. With this post I want to share my opinion on what a possible Assemblathon 3 could and/or should be about.

My review of “MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island”

Earlier this week, the first paper was published describing the use of Oxford Nanopore MinION data to solve a biological question. The paper, entitled “MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island” came out in Nature Biotechnology (ReadCube link).

I was a reviewer for this manuscript. I have posted my two (signed) review reports on publons. As data and code were made available by the authors (as it should be), I made a (mostly successful) effort to reproduce the computational part of the paper. After I was done with the review report of the second version I could not help myself to have a further look at some of the results. This led to me sending some plots to the authors, and one of these plots ended up becoming figure 1. This was a lot of fun to see in the final version.

Below are some excerpts of the review reports.

Our review of “Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data”, aka the HGAP paper

As it is out in the open that I was one of the reviewers of the ‘HGAP’ paper, I though I could as well make my review publicly available.

I have posted the review report (from February 2013) online at Publons. The review was actually done together with a PhD student in the group, Ole Kristian Tørresen (I like to do reviews together with others, it leads to better reviews and is a great learning experience for students!).

Here are the first few paragraphs. Enjoy!

My review of “Automated ensemble assembly and validation of microbial genomes”

Last month, a new paper appeared in BMC Bioinformatics, entitled “Automated ensemble assembly and validation of microbial genomes”. In it, the authors describe iMetAMOS, a module of the metAMOS package, for bacterial genome assembly. I was one of the reviewers (I signed my review), and post part of my review here. The full review can be found on publons.

iMetAmos workflow. From the paper, doi:10.1186/1471-2105-15-126

I signed my review because I believe in non-anonymous peer review (see Mick Watson’s “reviewer’s oath”).

I made my review available on publons, a platform to post pre- and post-publication peer-review reports after the article has been published, because I believe in open peer-review. EDIT Adam Phillippy, the senior author on the paper, posted the authors response to the review reports they received as a comment to review on publons!

I post the first part of my review here because it nicely summarises the paper and my (favourable) opinion of it. I’ll admit that I wrote these paragraphs of the review report with the idea of posting them to my blog 🙂

Enjoy!

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