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Why:

Technology/Technical Talks to learn, explore best practices from innovators, practitioners and exemplar projects that have relevance to iPlant activities

What:

45 min presentation followed by 15 min Q&A

When:

Regular talks are scheduled alternating Wed. at 12:00 Pacific/3:00 Eastern , depending on availability of presenters and their home timezone we also schedule ad-hoc sessions

Where:

Hosted from Keating 433 at UA, WebEx varies by talk

WebEx:

Web connection details are here (Note: see the URL/Link column in case there are issues connecting)

Who:

All interested developers, scientists and team members.

Upcoming Tech Talks for 2013 fall

Date 

Presenter

Institution/Title

Host

URL/Link

Abstract/Notes

Wed., Dec 4, 2:00 PM EDT

Maryanne Martone

Neuroscience Information Framework/Using Ontologies to Build a Semantic Search Portal: Lessons for making do with limited ontology resources

Ramona Walls





 

 

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

Nirav Merchant

http://thedata.org/

 

 

Wed., Oct 23, 3:00 PM EDT

Jim Myers

UMich/SEAD: Sustainable Environment Actionable Data

Damian Gessler

http://sead-data.net

 

 

Wed., Oct 9, 3:00 PM EDT

Philippe Rocca-Serra

Oxford e-Research Centre/ISA Tools: Biosharing Portal for Metadata Standards and Working with Publishers

Ramona Walls

 

 

Wed., Sep, 25, 3:00 PM EDT

Greg Wilson

Mozilla Foundation / Software Carpentry

Nirav Merchant

http://software-carpentry.org/

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

Ilya Baldin

RENCI/Programmable Cloud and Networks: The ExoGENI Project

Nirav Merchant

ExoGENI

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

Jeff Cavner

LifeMapper: Spatial Data Infrastructure (SDI) for biologists

Ramona Walls

Lifemapper
Webex:
1. Go to https://iplant.webex.com/iplant/j.php?ED=263910092&UID=1624279482&PW=NODU3ZTM2NDZl&RT=MiM1
2. If requested, enter your name and email address.
3. If a password is required, enter the meeting password: iPC123
4. Click "Join".

 

Wednesday, May 22
3 PM EDT

Tim Swaller, Ceres

Persephone: visualizing genomic data

Nirav Merchant

Webex Info

Recording of Presentation

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

Martha Narro

WebEx Info

Recording of Presentation

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

Martha Narro

WebEx Info

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.