news.

• Paper with Wayne Pfeiffer (SDSC) on the hybrid MPI/Pthreads parallelization of RAxML accepted for publication at HICOMB 2010 workshop which is held in conjunction with IPDPS 2010
• Fernando Izquierdo joins the Exelixis Lab as PhD student :-)
• According to Scopus which is an ISI-like citation tool, Alexis' 2006 Bioinformatics paper on RAxML-VI ranks on place 4 of the 20 most cited papers in Computer Science in the last 5 years (2006-2010)

• Paper accepted at RAW workshop which is held in conjunction with IEEE IPDPS 2010 conference. N. Alachiotis, A. Stamatakis: "Efficient Floating-Point Logarithm Unit for FPGAs"
• Two papers accepted for publication at 8th ACS/IEEE International Conference on Computer Systems and Applications (AICCSA-10), Hammamet, Tunisia, May 2010:
• S.A. Berger, A. Stamatakis: "Accuracy of Morphology-based Phylogenetic Fossil Placement under Maximum Likelihood"
• A. Stamatakis, Z. Komornik, S.A. Berger: "Evolutionary Placement of Short Sequence Reads on Multi-Core Architectures"
• Extended journal version of the RECOMB09 paper on "How many Bootstrap Replicates are necessary?" with N. Pattengale, M. Alipour, O.R.P. Bininda-Emonds, B.M.E. Moret, and E.J. Gottlieb accepted for publication at Journal of Computational Biology.

• The joint EMBO summer school grant application with Aidan Budd, Ziheng Yang, Nick Goldman, and Giorgos Kotoulas for organizing a 10-day school on "Molecular Evolution" at the Hellenic Center for Marine Research in Heraklion, Crete, Greece (May 2010) just got funded :-)  more details to follow soon.

• Prof. Ziheng Yang will be visiting us from December 1 - December 7
• Two PhD positions in phyloinformatics available at ETH Zurich in the group of Maria Anisimova, one of my favorite colleagues :-), more info here

• Paper on "Assessing the root of bilaterian animals with scalable phylogenomic methods"  accepted at Proceedings of the Royal Society  B.
• The iPTOL project web pages have been updated, including a detailed description of the working groups
• The DFG will kindly fund an additional PhD project that will deal with extremely large-scale tree reconstruction methods in conjunction with iPTOL
  

• RAxML reaches over 6,000 source-code downloads from distinct IPs, over 40,000 job submissions to the two web-servers, and over 500 citations from the 2005 Bioinformatics, 2006 Bioinformatics, and 2008 Systematic Biology papers
• Single versus double precision arithmetics again: I played around a bit more with RAxML to figure out the cases where it is worth to use single precision. I ran the SSE3-vectorized Pthreads version (16 threads on a Sun x4600) of RAxML on a protein dataset with 321,145 distinct alignment patterns and 232 taxa. The double-precision runs were done under GAMMA and the single-precision runs under CAT. This means that the memory footprint was at approx. 40GB for GAMMA under double precision and only at approx. 5GB for CAT under single precision. The CAT+single precision run was 3 times faster and also returned a tree with a slightly better likelihood when scored under GAMMA.
  
• Prof. Apostolos Dollas, Nikos' former supervisor at the Technical University of Crete, will be visiting us on July 20

• New, significantly faster version of RAxML has been released that also includes some advanced search mechanisms for trees with thousands of taxa
• Minh, a PostDoc at Arndt's lab in Vienna will be visiting us on July 9 & 10
• Paper on "Accuracy and Performance of Single versus Double Precision Arithmetics for Maximum Likelihood Phylogeny Reconstruction" accepted for publication at PBC09 workshop.

• Short paper accepted at FPL 2009 "A Reconfigurable Architecture for the Phylogenetic Likelihood Function" with Nikos Alachiotis, Apostolos Dollas, and Evripidis Sotoriades
• Two papers accepted at ICPP 2009

1. "Load Balance in the Phylogenetic Likelihood Kernel" with Michael Ott
2. "Fine-grain parallelism using Multi-core, Cell/BE, and GPU systems: Accelerating the Phylogenetic Likelihood Function" with Frederico Pratas, Leonel Sousa, and Pedro Trancoso

• Alexis is now a member of the EES (Munich Graduate School for Evolution, Ecology, and Systematics) school curriculum commitee at the Ludwig Maximilians University of Munich (Biology Department)

• There are HiWi positions for CS/Bioinformatics students available at Gert Wörheides Lab
• The NSF iPlant Collaborative Grand Challenge Proposal (PDF) received a very positive review. Alexis Stamatakis is a Co-PI on this grant which is lead by Mike Sanderson together  with Pam & Doug Soltis, Michael Donoghue, Todd Vision, and Val Tannen
• We moved to our new offices in finger number 9, 1st floor of the CS building
• New version of RAxML released with many new features
• Antonis Rokas and Casey Dunn visited us at Munich and gave very interetsing talks
• Fritz Sedlazeck, a PhD student from Arndt von Haeseler's lab in Vienna visited us to defend his PhD proposal
  

• Zsolt Komornik, an Erasmus student from France started working with us

• Nikos and Simon arrived at the Exelixis lab :-)
• Together with Susanne Renner we just finalized the program of the Symposium on "Advances in Tree Reconstruction from Complex Data Matrices" we are organizing. It will take place at the 2009 evolution meeting in Darwin's 200th birthday year. Symposium Speakers are: Mike Sanderson, Nick Goldman, Olivier Gascuel, Alexis Stamatakis, Casey Dunn, Derrick Zwickl, and Stephen Smith
  

• Paper on mapping the phylogenetic likelihood function on FPGAs entitled "Exploring FPGAs for accelerating the Phylogenetic Likelihood Function" co-authored with Nikos Alaxiotis, Evripidis Sotiriades, and Apostolos Dollas accepted for publication at HICOMB 2009 (held in conjunction with IPDPS2009)
• Paper on a phylogenetic bootstrap convergence criterion "How Many Bootstrap Replicates are Necessary?" co-authored with Nick Pattengale, Masoud Alipour, Olaf Bininda-Emonds, and Bernard Moret accepted for publication at RECOMB 2009
• New beta-version of the CIPRES portal (offering RAxML and many other applications for phylogenetic analysis) that provides a full workbench 

• On March 02 2009 we will organize a "Joint Exelixis Lab (TUM) & Molecular Palaeobiology/GeoBioCenter (LMU) Phylogenomics Seminar" together with Prof. Gert Wörheide at the GeoBioCenter. Antonis Rokas (Vanderbilt University) and Casey Dunn (Brown University) will give invited talks.
• RAxML surpasses 4,000 source code downloads from distinct IP addresses (total > 11,000)
• Ziheng Yang (University College London, Fellow of the Royal Society) will be visiting the Exelixis lab once per year within the framework of a BBSRC project on which we are collaborating, we are really looking forward to his visits
• SC08 cluster challenge article at insideHPC.com
• Szymon Seliga, an Erasmus student from Poland will join the lab as student programmer (HiWi)

• PRIB2008 paper was a finalist for the best paper award, Michael Ott presented this work at Melbourne, Australia
• The Exelixis Lab will move to the CS department of the Technical University of Munich
• Nikos succesfully defended his Diploma Thesis

• Simon Berger and Nikos Alahiotis will join The Exelixis Lab as PhD students

• RAxML will be one of the test applications for the IEEE/ACM 2008 Supercomputing Conference cluster challenge