Key Bioinformatics Computer Skills

I’ve been asked several times about which computer skills are critical for bioinformatics. Important – note that I am just addressing the “computer skills” side of things here. This is my list for being a functional, comfortable bioinformatician.

  1. SQL and knowledge of databases. I always recommend that people start with MySQL, because it is crossplatform, very popular, and extremely well developed.
  2. Perl or Python. Preferably perl. It kills me to write this, because I like python so much more than perl, but from a “getting the most useful skills” perspective, I think you have to choose perl.
  3. basic Linux. Actually, being at a semi-sys admin level is even better. I always tell people to go “cold turkey” and just install Linux on their computer and commit to using it exclusively for a while. (Due to OpenOffice etc, this should be mostly doable these days). This will force a person to get comfortable. Learning to use a Mac from the command line is an ok second option, as is Solaris etc. Still, I’d have to say Linux would be preferred.
  4. basic bash shell scripting. There are still too many cases where this ends up being “just the thing to do”. And of course, this all applies to Mac.
  5. Some experience with Java or other “traditional languages” or a real understanding of  modern programming paradigms. This may seem lame or vague. But it is important to understand how traditional programming languages approach problems. At minimum, this ensures some exposure to concepts like object-oriented programming, functional programming, libraries, etc. I know that one can get all of this with python and, yes, even perl – but I fear that many bioinformatics people get away without knowing these things to their detriment.
  6. R + Bioconductor. So many great packages in Bioconductor. Comfort with R can solve a lot of problems quickly. R is only growing; if I could buy stock in R, I would!

This may seem like a lot, but many of these items fit together very well. For example, one could go “cold turkey” and just use Linux and commit to doing bioinformatics by using a combination of R, perl and shell scripting, and an SQL-based database (MySQL). It is very common in bioinformatics to link these pieces, so… not so bad, in the end, I think.

As always, comments welcome…

Jobs: Graduate Student Funded Position available

I just want to write a short note that a FUNDED position is still available for a masters or Ph.D. student who would be a joint student with my lab and that of Gordon Chua here at University of Calgary. This is the same position posted earlier, so click the Jobs category and look at the previous posting…

I do think this would be an exciting and challenging position (but of course I do).

Jobs: Masters or Ph.D. Student for great genomics project

here is the ad that I have been posting:

Masters/Ph.D. Student
Leading-Edge Genomics and Bioinformatics
Systems Biology of Fission Yeast

Description:
This is a great opportunity for a motivated student interested in leading-edge genomics and bioinformatics. The laboratories of Gordon Chua, Ph.D and Mark Bieda, Ph.D. are looking to train a joint student who would use systems biology approaches to understand the genomic circuitry in fission yeast. Fission yeast is an ideal model for these studies, combining the complexity of a eukaryote system with the ability to easily perform genetic manipulations. The relatively small genome of fission yeast presents opportunities to do comprehensive large scale genomic studies. The work would involve a large variety of current genomic technologies, including large-scale microarray work. Gordon Chua recently received a five-year CIHR grant to perform this work. The student would perform experimental work in an experienced yeast lab (Gordon Chua) and bioinformatics analyses in the Bieda lab. This position offers a rare opportunity to receive excellent experimental and bioinformatics training while working on the frontiers of science.

The PIs are committed to developing the careers of members of the laboratory.

To apply or for more information, please email:

Mark Bieda, Ph.D. mbieda at ucalgary dot ca
Or
Gordon Chua, Ph.D. gchua at ucalgary dot ca

Jobs: Postdoctoral Positions in my lab

Update: I just hired an experimental postdoc – thanks to all that applied – and I am temporarily suspending the search for a computational postdoc.

I’m looking for two postdocs: one computational (bioinformatics) postdoc and one molecular biology postdoc.

I just posted this ad to naturejobs, so here is the info:

Positions:

2 Postdoctoral Positions Total

1 Computational (Bioinformatics) Postdoctoral Fellow

1 Experimental (Molecular Biology) Postdoctoral Fellow

Description:

These positions are in the laboratory of Mark Bieda. The lab focuses on (1) development of novel statistical and computational approaches to ChIP-seq and ChIP-chip data and (2) investigating the changes in chromatin marks in cancer using chromatin immunoprecipitation and related molecular biology approaches. These positions offer an excellent opportunity for cross-training (e.g. bioinformatics training for an experimentalist, experimental training for a computational postdoc).

Bioinformatics Position: The computational position will focus on novel statistical and algorithmic methods for analysis of microarray (ChIP-chip) and high-throughput sequencing (ChIP-seq) experiments. This project will afford the opportunity for large-scale experimental validation of predictions within the lab. The successful computational candidate will be comfortable thinking statistically and have good programming skills with a keen interest in large-scale data analysis. Experimental Position: The experimental position will focus on examining chromatin organization in brain tumor models (primarily gliomas). There is also opportunity for work on other projects in neurogenomics. Previous experience/familiarity with neuroscience is a plus, but not required. The successful candidate will have experience with a wide range of molecular biology techniques.

Both positions offer opportunities for both formal collaborative and informal interactions with other strong research groups, including a very active Brain Tumor Group at the university. The PI is committed to developing the careers of members of the laboratory.

The University of Calgary offers an excellent environment with a rapidly growing pool of biomedical research labs and significant shared facilities. We encourage all qualified persons to apply. The University of Calgary hires on the basis of merit and is committed to employment equity. However, Canadians and permanent residents of Canada will be given priority.

Calgary is a city of ~1 million people and is located only about 1.5 hours from world-renowned recreational areas (Banff and Jasper).

To apply, please send (1) cover letter, (2) CV and (3) names and contact information for three references to Aarif Edoo (aedo@ucalgary.ca). PDF format for application materials is preferred. Letters should be addressed to Mark Bieda, Ph.D.