A nice TV interview in German by Alexis' PhD advisor Arndt Bode on supercomputing in Munich.
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:
stepwise addition order algorithm
branch length optimiziation
The tool requires JAVA and can be downloaded here.
To execute the code, download it, unccompress it and type:
The input files are log files generated from real RAxML runs. You can see a screenshot below.
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).
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:
Elisa Loza wrote a vrey nice and understandable
blog post about RAxML and the evolutionary placement algorithm.
Agniezska Borowska from HITS produced a very nice video about
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.
What do Exelixis lab members actually do all day long?
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
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
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:
Local Cretan TV (Kriti TV) report about 2012 summer school on
computational molecular evolution sponsored by EMBO and co-sponsored by
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
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
As a spinoff of our summer school on computational molecular evolution
in Crete (May 2010), an African participant organized a video-conference based course
across Africa including some of the lecturers from the Cretan summer
by local Cretan TV channel "Kriti TV" about the EMBO summer school on
computational molecular evolution at IMBG-HCMR, Heraklion, Crete in May
2010. Giorgos Kotoulas (IMBG-HCMR, Greece), Antonis Rokas (Vanderbilt
Univ., USA), Alexandros Stamatakis (TU München, Germany) and Nick
Goldman (European Bioinformatics Institute, UK) are interviewed. I will
try to add subtitles when I find the time.
My colleague in Munich Gert Wörheide hunting living fossils on German
Public TV (German only): Video
More information about this project can be found here
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
area of phylogenomics. The Exelixis Lab (Michael Ott and Alexandros
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.
with Susanne Renner I gave an outreach talk on phylogenetic
reconstruction within the framework of the Munich Science Days at the
LMU Munich which are open to the broad public. The slides of this talk
are available here for download as PDF.