Upcoming Tech Talks for 2013 fall
Wed., Dec 4, 2:00 PM EDT
Neuroscience Information Framework/Using Ontologies to Build a Semantic Search Portal: Lessons for making do with limited ontology resources
Wed., Nov 6, 3:00 PM EDT
Tom Carsey/Jonathan Crabtree
UNC-Odum Institute/DataVerse: Open Source Application to Publish, Share, Reference, Extract, and Analyze Research Data
Wed., Oct 23, 3:00 PM EDT
UMich/SEAD: Sustainable Environment Actionable Data
Wed., Oct 9, 3:00 PM EDT
Oxford e-Research Centre/ISA Tools: Biosharing Portal for Metadata Standards and Working with Publishers
Wed., Sep, 25, 3:00 PM EDT
Mozilla Foundation / Software Carpentry
Over the last 15 years, Software Carpentry has evolved from a week-long training course at the US national laboratories into a worldwide volunteer effort to raise standards in scientific computing. This talk explores what we have learned along the way the challenges we now face, and our plans for the future.
Wed., Sept 11, 3:00 PM EDT
RENCI/Programmable Cloud and Networks: The ExoGENI Project
ExoGENI: Networked Infrastructure-as-a-Service (NIaaS) for Scientific Workflow Applications.ExoGENI is a GENI testbed that links GENI to two advances in virtual infrastructure services outside of GENI: open cloud computing and dynamic circuit fabrics. ExoGENI orchestrates a federation of independent cloud sites (i.e. OpenStack and Eucalyptus sites) and circuit providers (i.e. NLR and Internet2) through their native IaaS API interfaces and links them to other GENI tools and resources. In this talk, we will present our current efforts and capabilities to enable the execution of complex data-driven workflows across geographically distributed sites. First, we will present the high-level capabilities and architecture of ExoGENI and the Open Resource Control Architecture (ORCA)software layer that powers ExoGENI. Second, we will describe the advanced virtualization mechanisms (SDN, storage, I/O) leveraged by our testbed that are crucial for efficient data sharing and processing. Finally, we will discuss our work toward the integration of our system with a state-of-the-art workflow engine (Pegasus) and some interesting long-lived workflows currently running on ExoGENI. We will conclude with discussion on the future direction of our work.
Wed., Sept 4, 3 PM EDT
LifeMapper: Spatial Data Infrastructure (SDI) for biologists
Wednesday, May 22
Tim Swaller, Ceres
Persephone: visualizing genomic data
Persephone™ is a software application for visualization and analysis of genomic data. It has been designed to display diverse data such as genetic maps, genomic sequences, gene models, synteny, QTLs, SNPs, RNA-seq, and gene expression. The application presents genomes as sets of maps. A map can be based on marker positions (genetic maps) or a genomic sequence (physical maps).The user can align maps of different types, which makes the application valuable for those who work with species that are not yet completely sequenced. Our technology allows zooming from a chromosome bird's-eye view down to the nucleotide level. The SNP track visualizes individual genotypes along with the reference sequence and assists in the derivation of haplotypes. The QTL search narrows a large volume of QTLs down to a filtered set of studies based on given criteria, such as target traits or treatments
2PM EDT, Monday, March 25
Brody Sandel, Aarhus University
Patterns of Phylogenetic Diversity in New World Plants
Large scale patterns of phylogenetic diversity are not well understood for most groups of organisms. This is in part because of data availability and computational limitations. Distributional and phylogenetic data are needed for large numbers of species, and even given these data, traditional computational methods often cannot accommodate the resulting large data structures. In this talk, I use the BIEN distribution and phylogenetic data for more than 80000 New World plants to overcome data limitations, and novel algorithms and analytical approaches to overcome computational limitations. The results are the first maps of phylogenetic diversity for such a large group of organisms over such a large geographic extent. These results can be used to understand the evolutionary origin of hotspots of plant richness.
2PM EST, Tuesday, Feb. 26
Brian Enquist, University of Arizona
Toward a General Informatics Engine to Quantify Botanical Diversity at Large Scales
The iPlant-BIEN collaboration has produced the TNRS, preliminary species range distribution maps for plants in the Americas, and, this summer, will release the BIEN 3.0 database which comprises the most comprehensive set of species observations and trait data for plants in the Americas.