COS Lectures
Die, 5. Jun 2012, 17:00, Dr. Alexandros Stamatakis: "Biodiversity Informatics: An Emerging Computational Science"
COS-Lecture
INF 360, lecture hall, Die, 5. Jun 2012, 17:00
Dr. Alexandros Stamatakis
Scientific Computing group, HITS gGmbH, Heidelberg
"Biodiversity Informatics: An Emerging Computational Science"
Abstract:
Biodiversity informatics and phyloinformatics in particular are currently
facing a paradigm shift toward becoming a 'real' computational science.
Molecular sequencing technologies are developing at a rapid pace, providing the biological sciences with enormous amounts of new data.
Due to the necessity to process (and store) huge amounts of data, we expect the field to undergo an analogous transition that physics or computational fluid dynamics underwent 20
to 30 years ago. For instance, we are already facing such data analysis challenges in the 1000 insect transcriptome sequencing project (www.1kite.org). Such evolutionary studies require software that scales far beyond a multi-core node, that can be checkpointed and restarted with low overhead, and that can accommodate
the memory requirements of whole-genome datasets under likelihood-based models.
As an example of the efforts to turn biodiversity informatics into a computational science, I will describe RAxML-Light,
a dedicated tool for large-scale phylogenetic inference on supercomputers under maximum likelihood.
RAxML-Light implements a light-weight checkpointing mechanism, deploys 128-bit (SSE3) and 256-bit (AVX) vector intrinsics, offers two orthogonal memory saving
techniques, and provides a fine-grain production-level MPI (Message Passing Interface) parallelization of
the likelihood function.
To demonstrate scalability and robustness of the code, we inferred a phylogeny on a simulated DNA alignment (1481 taxa, 20,000,000 bp) using 672 cores. This
alignment required one TeraByte of RAM to compute the likelihood score on a single tree.
Web: www.exelixis-lab.org
Die, 12. Jun 2012, 17:00, Prof. Dr. Sacha Baginsky: "Functional proteomics: The role of posttranslational modifications in chloroplast biogenesis and function"
COS-Lecture
INF 360, lecture hall, Die, 12. Jun 2012, 17:00
Prof. Dr. Sacha Baginsky
Institut für Biochemie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale)
"Functional proteomics: The role of posttranslational modifications in chloroplast biogenesis and function"
Die, 26. Jun 2012, 17:00, Dr. Pascal Genschik: "When protein degradation meets RNA silencing"
COS-Lecture
INF 230, small lecture hall, Die, 26. Jun 2012, 17:00
Dr. Pascal Genschik
Institut de Biologie Moléculaire des Plantes, CNRS, Strassboug, France
"When protein degradation meets RNA silencing"
Die, 10. Jul 2012, 17:00, Dr. Christa S. Testerink: "Take it or leave it: cellular signaling pathways linking salinity stress to root growth"
COS-Lecture
INF 230, small lecture hall, Die, 10. Jul 2012, 17:00
Dr. Christa S. Testerink
Swammerdam Institute for Life Sciences, University of Amsterdam,
NL
"Take it or leave it: cellular signaling pathways linking salinity stress to root growth"
Past COS-Lectures
08.03.2012, 10:00 Uhr, kleiner Hörsaal, Im Neuenheimer Feld 230Dr. Devos, Damien, Structural Bioinformatics , EMBL Heidelberg
Microbiology's Platypus
01.03.2012, 17:00 Uhr, Hörsaal 041, Im Neuenheimer Feld 267 (Bioquant)
Prof. Dr. Steele, Rob, Department of Biological Chemistry, School of Medicine, University of California, Irvine, USA
Exploring Hydra development using genomics and chemical genetics
01.03.2012, 11:00 Uhr, kleiner Hörsaal, Im Neuenheimer Feld 230
Prof. Dr. Foulkes, Nicolas S., COS Heidelberg, Universität Heidelberg und ITG, KIT
Circadian Clocks and Photoreception: Lessons from Fish
14.2.2012, Lecture Hall Im Neuenheimer Feld 360
Prof. Liu, Jian-Quan, Lanzhou University, China
Introgression and hybrid speciation in Ostryopsis (Betulaceae)
07.02.2012, Small Lecture Hall Im Neuenheimer Feld 230,
Dr. Robatsek, Silke, Sainsbury Lab, Norwich, Großbritannien
Plants communicating with pathogens: membranes in motion and cellular responses
20.12.2011, Lecture Hall Im Neuenheimer Feld 360,
Prof. Dr. Mummenhoff, Klaus, Universität Osnabrück
Evolutionary studies in Brassicaceae: Molecules and Morphology meet Ecology
15.11.2011, Lecture Hall Im Neuenheimer Feld 360
Prof. Dr. Feussner, Ivo, University of Göttingen
On the quest for biomarkers for Verticillium infection
09.11.2011, Lecture Hall Im Neuenheimer Feld 360
Dr. Ryals, John, Metabolon Inc., Durham, USA
Metabolomics applications for mechanistic insights and biomarker discovery
08.11.2011, Small Lecture Hall Im Neuenheimer Feld 230,
Prof. Dr. Hofius, Daniel, Uppsala BioCenter, Schweden
Mechanisms of autophagy and programmed cell death in plant immunity
25.10.2011, Lecture Hall Im Neuenheimer Feld 360
Prof. Dr. Menon, Anant, Weill Cornell Medical College, New York, USA
Lipid flipping and N-glycosylation
20.10.2011, Lecture Hall Im Neuenheimer Feld 360
Ass. Prof. Dr. Geitmann, Anja, Université de Montréal, Canada
Shaping up - the challenge of making a tube
Dr. Wolf, Sebastian, INRA, Versailles, Frankreich
Sensing of cell wall integrity
10.10.2011, Small Lecture Hall Im Neuenheimer Feld 230
Prof. Dr. Mathur, Jaideep, University of Guelph, Canada
Differential colouring for understanding rapid sub-cellular responses in plants