The Exelixis Lab


Enabling Research in Evolutionary Biology

Outreach activities

Videos

A TV report by the nano technology magazine of 3Sat about the work of our group in the framework of the 1KITE project.

Alexis gave a video interview (in German) about his new duties as professor of computer science at KIT in conjunction with his position at HITS.

The video below was shot for the NSF-funded iPlant (infrastructure for plant sciences) project.

Local Cretan TV (Kriti TV) report about 2012 summer school on computational molecular evolution sponsored by EMBO and co-sponsored by HITS.


Local Cretan TV (Kriti TV) report about 2010 summer school on computational molecular evolution sponsored by EMBO:

Agniezska Borowska from HITS produced a very nice video about phylogenetic inference:

Newspapers and press releases

Alexis gave a newspaper interview to the Greek newspaper Kathimerini about the crisis and Greek researchers abroad. The drawing below by Titina Xalmatzi was also part of that interview. Here is a rough German Translation (due to lack of more time to do it properly).


An article about the work of our group was published in a local newspaper.

Press releases on big plant tree with 55,000 species English German

A very readable and easy to understand article was published in Genome Web. It addresses High Performance Computing for Phylogenetics and some of the work conducted at the Exelixis Lab.

Our work is briefly mentioned on pages 68-69 in the 2009 yearbook of the German Science Foundation (DFG)

Elisa Loza wrote a vrey nice and understandable blog post about RAxML and the evolutionary placement algorithm.

A press release (German only) was published jointly by TUM/LRZ on the integration of RAxML into the SPEC MPI 2007 benchmark.

Disentangling the evolution of metazoa: Here is a press release by Brown University in English and a press release by TU Munich in German describing some recent work in the area of phylogenomics. The Exelixis Lab (Michael Ott and Alexandros Stamatakis) significantly contributed to this project by providing and adapting the software, organizing the computational resources, and conducting the large-scale inferences on a IBM BlueGene/L supercomputer system at the San Diego Supercomputer Center.

A news item about Alexis appointment at the Karlsruhe Institute of Technology

A news item about the recent Nature Methods paper with the Bork lab at EMBL. In this paper we apply our Evolutionary Placement Algorithm to disentangle and quantify bacterial diversity.

Outreach Material and Links

A nice TV interview in German by Alexis' PhD advisor Arndt Bode on supercomputing in Munich.

An excellent collection of outreach videos describing why evolution (and as a consequence the tools and software we are developing) is important in many areas of our daily life: Evolution of Life Web-Site

A radio interview with Bernhard Misof (in German) about the 1KITE project (1000 insect transcriptome sequencing project): STREAM
Also have a look at two local newspaper articles about 1 Kite from Hamburg and the Rhein-Neckar Region

Some slides from an outreach talk on phylogenetics (in German): PDF given by Alexis in May 2011.

Our colleague in Munich Gert W├Ârheide hunting living fossils on German Public TV (German only): Video. More information about this project can be found here

Together with Susanne Renner Alexis gave an outreach talk on phylogenetic reconstruction within the framework of the Munich Science Days (in October 2008) at the LMU Munich which are open to the broad public. The slides of this talk are available here for download as PDF.

Geek Stuff

Tree Building Outreach tool

Tree reconstruction visualization outreach tool. Matthias Berger, the brother of our former PhD student Dr. Simon Berger has designed a visualization tool that displays the tree building phases of RAxML:

  1. stepwise addition order algorithm
  2. SPR moves
  3. branch length optimiziation
The tool requires JAVA and can be downloaded here. To execute the code, download it, unccompress it and type:

java -jar treevis.jar --tracefile test-data/combined_log.txt

or

java -jar treevis.jar --tracefile test-data/dump_49.txt

The input files are log files generated from real RAxML runs. You can see a screenshot below.


RAxML on Android

Get the new RAxML code (the main code developed by our lab ) for your Android phone here

It doesn't serve any purpose except for impressing your colleagues and friends by being an early technology adopter and running a scientific code on your smartphone, screenshots below:


What does the lab actually do?

Our main focus is on developing better models and faster software such that biologists can analyze their constantly growing datasets more quickly and more accurately. Hence, we spend quite a large fraction of our time writing code (mostly in C and C++ but occasionally also in JAVA, ruby, or perl). We are all big fans of open source code and provide everything we code up for free under the GNU GPL open source license.

To write and share sooftware (code) we use web-based tools that have a code version control, that is, if we implement a new bug rather than a feature (which happens more frequently than you would think) we can actually roll-back and re-start from a working code (a less buggy code).

Typically, we use the GIT version control system that is available free of charge as a web-service on platforms such as github. Those platforms can be used free of charge for public open source code projects. Below you will find a list of links to the github starting pages of some lab members such that you can see and follow live what we are doing:

Alexis
Andre
Simon
Jiajie
Tomas
Fernando