“Programming for Evolutionary Biology” course – suggestions for the applicants that have not been accepted

Posted on February 16, 2012 by Giovanni Marco Dall'Olio

The selection phase for the participants to the “Programming for Evolutionary Biology” course in Leipzig has finished. Congratulations to all the applicants accepted!

I am very sorry for the people who have not been accepted, but we have received a lot more applications than the places available, and the selection process has had to be very strict. As Katja Nowick, the organizer of the course, said, this is a sign of how much introductory courses to programming for researchers are needed. Hopefully we will be able to repeat the course or other people will organize similar courses in the future.

In case you have not been selected, I would like to give you a few suggestions on how to start to learn Unix/R/Perl skills.

- Are there any other courses for learn Programming oriented to biologists?

I think that the “Unix and Perl Primer for Biologists” course is a very good resource for researchers wishing to learn the basics of the Bash shell and Perl. Their material is easy to read, and explains everything step by step. The authors also wrote a book (which I didn’t read yet), and released some good material on this website.

Another good course that should not be missed is “Software Carpentry for Biologists“. This course covers a wider range of topics than the other, and, more important, dedicates a good effort on explaining what should be the “good practices” for a bioinformatician. Maybe the contents are a bit more advanced than the “Unix and Perl Primer”, although there are classes on the shell. In any case, once you feel a bit confident on your programming skills, you should definitely read all the materials on Software Carpentry, and make sure you have understood everything before starting a research project. There is also an “Advanced Software Carpentry for Bioinformaticians“, by Titus Brown, focused on Python programming.

- Are there other courses on Programming for Evolutionary Biologists, or on Next Generation Sequencing?

Thanks to reddit/bioinformatics, I have found two other courses similar to ours: a “Workshop on Molecular Evolution” from the University of Texas, and a “Computational molecular evolution” Course from EMBO in Greece. Both these courses seem very valid, although I don’t have any direct experience with them.

A good course on Next Generation Sequence is the Angus course, by Titus Brown. Titus Brown is a skilled bioinformatician and programmer, who developed, among other things, libraries such as Pygr and parts of nosetests. The website of the course is full of good documentation and examples, it should be a good place to start.

- where can I get help?

Internet is a good place where to ask for help on programming related questions. The StackOverflow network is the most active community for anything related to Programming and Unix in general. For next generation sequencing analysis, a good place is SeqAnswers. And, for the general bioinformatics question, biostar is of course a nice resource :-)

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Origins of Evolutionary Innovations, chapter 3

Posted on February 10, 2012 by Giovanni Marco Dall'Olio

Here is the third chapter of “Origins of Evolutionary Innovations”! This chapter describes innovations in regulatory systems, and the evolution of networks of transcription factor sites.

The most important message of this chapter is that regulatory circuits can suffer a lot of changes, and yet remain functional. For example, some researchers have change up to 600 transcription factors in E.coli, yet it was still able to survive. Or, as another nice example, galactose metabolism is regulated by two completely different transcription factors in S.cerevisiae and C.albicans, yet these two species are not so distant philogenetically.

Another important message of this chapter is the structure of genotype networks of metabolic circuit. I think it can be well represented by this figure taken from [1]. It represents that, in order to find new phenotypes, a genotype network must be robust to changes (all the possible genotypes must be connected), but also be large, so it is able to explore the genotype space.

[1]Ciliberti, S., Martin, O., & Wagner, A. (2007). Innovation and robustness in complex regulatory gene networks Proceedings of the National Academy of Sciences, 104 (34), 13591-13596 DOI: 10.1073/pnas.0705396104

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Origins of Evolutionary Innovations, chapter 2

Posted on February 3, 2012 by Giovanni Marco Dall'Olio

In the second chapter, Wagner discusses the variability of metabolic networks. How do metabolic networks evolve? How many reactions can I remove or add to a metabolic network, without altering its phenotype? How much the phenotype of a metabolic network is robust to changes?

A possible source of confusion in this chapter is the definitions used. The “metabolic network” is the set of all the reactions that an organism can catalyze; while the “genotype network” is the concept defined in the previous chapter. So, this chapter explains how “genotypes networks of metabolic networks” evolve; be careful to not confuse the two terms. The following figure from [1] can clarify the definitions:

1. Matias Rodrigues, J., & Wagner, A. (2009). Evolutionary Plasticity and Innovations in Complex Metabolic Reaction Networks PLoS Computational Biology, 5 (12) DOI: 10.1371/journal.pcbi.1000613

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Origins of Evolutionary Innovations, chapter 1

Posted on January 27, 2012 by Giovanni Marco Dall'Olio

We just finished the first session of the book “Origins of Evolutionary Innovations” by A. Wagner, on Chapter 1.

Click on “Continue Reading” to see a resume of this chapter.

Continue reading →

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book club on “Origins of Evolutionary Innovations” by A. Wagner

Posted on January 27, 2012 by Giovanni Marco Dall'Olio

I am organizing a discussion club on the book “Origins of Evoutionary Innovations” by A. Wagner, for my group.


Well, I don’t promise anything, but since I will do the effort of producing some presentations anyway, I will also publish all the slides here in this blog.

This book describes how new phenotypes are discovered in evolution. In the first chapter, it starts by describing some examples of notable phenotypes that have appeared, such as the Urea cycle and the ability to use glucose as a carbon source. But in general, this book is about how any novel phenotype appears in evolution.

It also explains the concepts of genotype space and genotype network, and how much variability can a population of organisms withstand without having changes in a given phenotype. For example, there are far more possible mRNAs than the number of proteins observed, so it seems that any given protein can be produced by more than one mRNA. This means that an organism can withstand many changes to its DNA, without suffering changes to the structure of the protein. What is the role of this variability in evolution?

There is also a nice paper published on the topic today, in Science: Meyer JR et al, Repeatability and Contingency in the Evolution of a Key Innovation in Phage Lambda, Science 2012.

The book club will take place only in my lab, but if you are interested, you can follow the slides and comment on this blog. (or would it be better to discuss it on Twitter? Let’s use the #evol_innov_book tag on twitter). Enjoy!

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Programming for Evolutionary Biology Course – Leipzig 2012

Posted on January 8, 2012 by Giovanni Marco Dall'Olio

This year I will teach in a two-week Introductory course to Programming and Bioinformatics, aimed at PhD students and Post-Docs working in Evolutionary Biology. This is a course designed for researchers that have little or no experience with programming, and it will teach them the basics of Bash, Perl, R Programming along with popular tools used in Evolutionary Biology.

The deadline for application is January 31st 2012, and the course will be held in Leipzig (Germany) in the last two weeks of March 2012. Please check the home page of the course for details on how to apply:

We tried to keep the cost of the course as low as possible, and thanks to a contribution from the Volkswagen foundation we have been able to keep it at only 300 euros for person. Plus, we have some fellowships available.

Here it is the programme, that you can also find in the home page of the course:

  • Introduction to Linux (Giovanni Marco Dall’Olio, University Pompeu Fabra, Barcelona, Spain)
  • Introduction to R (Katja Nowick, University Leipzig, Germany)
  • Analysis of next generation sequencing data (Tomas Marques-Bonet, University Pompeu Fabra, Barcelona, Spain)
  • Analysis of structural variants (Tomas Marques-Bonet, University Pompeu Fabra, Barcelona, Spain)
  • Analysis of expression data (Katja Nowick, University Leipzig, Germany)
  • Promoter evolution (Annalisa Marsico, Max-Planck-Institute for Molecular Genetics, Berlin, Germany)
  • Statistics & Inference (Stuart Baird, University Porto, Portugal)
  • Introduction to Perl (Sofia Robb, University of California Riverside, USA)
  • Phylogenomics (Rui Faria, University Porto, Portugal)
  • Ensembl API (Bert Overduin, EMBL – European Bioinformatics Institute, Hinxton, Cambridge, UK)
  • Introduction to databases (Jan Aerts, Leuven University, Belgium)
  • Visualization of scientific data (Jan Aerts, Leuven University, Belgium)

Invited speakers:

  • Evolution of behavior (Sarah London, University of Chicago, USA)
  • Evolutionary ecology (Claudia Acquisti, Westfälische Wilhelms-University Münster, Germany)
  • Phylogenomics (Rasmus Nielsen, University of California, Berkeley, USA)
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a script to fetch images from the UCSC browser

Posted on December 14, 2011 by Giovanni Marco Dall'Olio

The UCSC browser is a nice, useful but “mammoth-ish” bioinformatics tool that despite its web 1.0 aspect, can be a very powerful ally for any bioinformaticians or biologist.

I have to admit that for many years I avoided using the UCSC browser, dismissing it because of its very old fashioned look. It was silly of me to think that way, but its interface is objectively old: for example, the user is forced to reload the whole page to update the visualization, and the fonts are not anti-aliased, and they look ugly. To me, it didn’t seem “professional” to use a pre-Ajax website for doing research.

Recently, however, I have changed my mind about this, as I discovered that this tool can be very powerful to integrate data from different sources and for doing “mash-ups”. A local UCSC browser instance can be installed in a computer and be used as a central repository for all the annotations produced in a research unit: for example, sequencing data, results from experiments and from statistical genome-wide tests, etc. If all the custom annotations produced in a lab are available in a local UCSC browser instance (either as custom tracks or as tables), it is possible to compare them, and also to compare them against annotations available publicly, such as position of genes, non-coding regions and much more. The real strength of this tool is that if you have a workflow to automatize retrieval of data from it, you are able to compare your results with virtually anything that is known about a genome.

So, let’s go to the point: I wrote a script to automatically fetch screenshots of a UCSC browser instance. It is available at this page:

The first difficulty I faced when writing this script was that there are a lot of possible different options, to define a region and how to visualize it. So, I have made the script to require three different configuration files: one for the regions to be visualized, one for the tracks to be shown, and one for the connection parameters. So here it is how you would call it:

python fetch_ucsc.py --region <regions file> --tracks <tracks file> --config <connection configuration file>

Have a look at this pdf that created with this script. If you continue reading the post, I will also describe the different configuration files.

example of report created by this script. Click on the image to see the full pdf.

Continue reading →

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New ways to explore your academic impact

Posted on November 17, 2011 by Giovanni Marco Dall'Olio

It seems that today, for a strange series of coincidences, is a good day if you wanted new tools to explore your academic impact.

First, Google/Scholar Citations has finally been opened to all. Everybody can now create a profile on Google/Scholar, to keep track of articles and citations. I like google/scholar because it finds articles and books that are not indexed on scopus, but that are interesting nevertheless. Plus, it is free to use. However, our paper on Recombination Rates has been recently cited in a Nature Genetics paper, and Google/Scholar didn’t find it out.

Second, the finalists for the PLoS/Mendeley binary battle have been selected. Check the list here. The PLoS/Mendeley binary battle is an initiative proposed by these two organizations to encourage the writing of applications that make use the PLoS and the Mendeley APIs, to retrieve information on papers and readers. So, this initiative is originating some very good web applications to explore academic impact or play with citations and papers, and here I will describe some of my favourites.

I like two tools to see the impact of research articles on Internet: Total Impact and Readermeter. They both allow to see how many times your articles are read on Mendeley, cited, referenced on Twitter and Facebook, bookmarked on CiteULike, and much more.  The nice thing about Total Impact is that it also indexes my presentations on slideshare: for example, one of my presentations on Python is actually more popular than any other paper. However, one of our papers is not being recognized correctly, because of a duplicated entry in mendeley. On the other hand, Readermeter allows to see the geographical distribution of readers, and provides more statistics. It would be good if it would be possible to embed one of these two reports in a web page, for example in the About page of a blog, or an academic home page.

My TotalImpact report. Click on it to see the full report. Check also my ReaderMeter report if you like.

Another tool I liked is PaperCritic. It is a repository of commentaries on published papers. The idea is not entirely new: PLoS and other journals already allow to comment on papers. Unfortunately not all publishing houses provide this option.. moreover, having a central repository of comments on papers makes them easier to browse and select. I only wonder how much this tool is redundant with ResearchBlogging, and if the commentaries posted on the site are communicated to the authors of the paper even if they are not signed on PaperCritic.

So, these tools provides new ways to play with academic impact indicators, and to see whether our work is effectively useful to anyone.. I’ve played with them this morning, but now I would be better to get back to work, to improve their results :-)

 

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Twitting from the X CRG Symposium on “Computational Biology of Molecular Sequences”

Posted on November 10, 2011 by Giovanni Marco Dall'Olio

Today and tomorrow I will be attending a symposium organized here in Barcelona, about bioinformatics analysis of molecular sequences. Many well known bioinformaticians will participate, including Temple Smith (the Smith & Waterman algorithm), Amos Baroch from Expasy and Tim Hubbard from the EBI institute. Check the programme here, or the Streaming Video here.

The organization of this Symposium as been innovative in a “web 2.0 way”, as the participants have been able to interact in advance with the speakers, through a online web forum. For example, we have been able to propose to Tim Hubbard to explain how the concept of reference genome will evolve in the 1000genomes era, and, seeing that he has changed the title of his presentation, it seems that he is going to talk about it.

So, if everything goes well, I will be twitting from there… This is the first time I use twitter during a conference, so be kind with me :-) .

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Scifund projects online

Posted on November 1, 2011 by Giovanni Marco Dall'Olio

The Scifund initiative has reached its final phase. Now all the projects are publicly visible online on RocketHub.

click on the logo to go to the list of projects uploaded

I am surprised to see how many projects have been presented! The crowd-funding seems to be a good idea to make science, specially in these times of crisis. I will keep it in mind for when I will finish my PhD and start looking for a post-doc. If I won’t find any position soon, it seems to be a good way to obtain funding for a short research project, and survive a bit more :-) .

The blog of the initiative is very interesting. Here are some of my favorite posts so far:

  • the story of a successful case of crowdfunding for a research project
  • metaphors in science: how to use metaphors to describe complex scientific things to common people. For example, an electrophoresis can be explained as a thin forest that small and big animals have to cross.

And some projects I find interesting:

Continue reading →

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