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LA-SiGMA Workshop: Connecting data through semantics and ontologies: a pathway to open data in science, June 7-8, 2013


The LA-SiGMA project, with LSU's Center for Computation & Technology, the Environmental Molecular Sciences Laboratory of the Pacific Northwest National Laboratory (PNNL), and High Performance Computing at LSU, will be hosting their first Workshop on Semantic Physical Sciences, June 7-8, 2013, at Louisiana State University, in Baton Rouge, LA.

This Workshop will bring together leading scientists and practitioners in the field of semantic sciences for a two day session of lectures and discussions. It will provide the knowledge needed to write a strong NSF data plan or to participate in data sharing in your field. The Workshop will consist of a mixture of theoretical and practical elements and will cover areas including but not limited to:

Invited speakers are:

Nico Adams, CSIRO
Nico Adams is a Senior Research Scientist at the Commonwealth Scientific And Industrial Research Organisation (CSIRO), Australia's National Laboratory, where he leads some of the materials and manufacturing informatics efforts in the division of Materials Science and Engineering.
Nico read chemistry at the University of York (UK) and subsequently worked as a research chemist, first at DSM Research (NL) and later at Cambridge Combinatorial (now Millenium Pharmaceuticals) in the area of high throughput synthesis and screening of olefin polymerization catalysts.
In October 1999 he joined the Inorganic Chemistry Laboratory at the University of Oxford as a doctoral student and the group of Prof U. Schubert at the Eindhoven University of Technology/Dutch Polymer Institute as a Research Associate and project leader in materials informatics.
This was followed by a further appointment at the Unilever Centre for Molecular Science Informatics, University of Cambridge in the research group of Prof Peter Murray‚ÄźRust. During this period, he helped to develop Polymer Markup Language - an extension of Chemical Markup Language (CML) to describe polymers and associated data, as well as beginning the development of ChemAxiom - an ontological framework for chemistry.
This was followed by brief period at the Department of Genetics (University of Cambridge) and as a visitor at the European Bioinformatics Institute (EBI, Cambridge) where he worked on the ChEBI ontology and developed the Primary Immunodeficiency Disease Ontology before finally joining CSIRO in 2011.

Dave Cowley, PNNL
Cowley's primary research interests are in unique problems associated with architecting, engineering, and administering large scalable computer and data storage systems. He is the lead for EMSL's Molecular Science Computing capability. Primarily, he provides terascale supercomputing and petascale data storage services for EMSL users. His operations team performs engineering, as well as implementation and operations of high-end computing hardware, operating systems, and software. Since joining PNNL, Cowley has been managing large computer systems to support PNNL business and research. Since the early 1990s, he has been at the forefront of PNNL's UNIX and Linux system administration, instituting many practices that remain in use today. When he took responsibility for a 128-node IBM SP/2 supercomputer in the late 1990s, Cowley made the transition from business-oriented database server administration to high-performance technical computing. Following that success, he joined EMSL in 2001, where his technical work has focused on large-capacity commodity storage. He is the architect of three generations of the EMSL data archive.

Bert de Jong, PNNL
Bert leads the team at PNNL responsible for the development of the NWChem quantum chemistry software. NWChem is the leading one-of-a-kind open-source computational chemistry software capability within the DOE complex that delivers a massively parallel and scalable simulation toolkit on EMSL's Chinook supercomputer with unique capabilities that fully integrate with the experimental capability suite at EMSL. The software is available to the community under the open-source Educational Community License 2.0 (ECL 2.0). The open-source web pages can be found at http://www.nwchem-sw.org.
One of Bert's interests is the integration of experiment and simulation. He is working on the development of a semantically enriched NWChem software suite based on the Chemical Markup Language and the FoX XML writer library. Bert is using prototypes to integrate data from relativistic computational chemistry NMR simulations with experimental data to understand the fundamental bonding properties of heavy element species and materials.

Marcus Hanwell, Kitware Inc.
Marcus D. Hanwell is a Technical Leader in the Scientific Computing group at Kitware, Inc. He leads the Open Chemistry project (http://openchemistry.org/), which focuses on developing open-source tools to for chemistry, bioinformatics, and materials science research. He completed an experimental PhD in Physics at the University of Sheffield, a Google Summer of Code developing Avogadro and Kalzium, and a postdoctoral fellowship combining experimental and computational chemistry at the University of Pittsburgh before moving to Kitware, Inc. in late 2009. He is a member of the Blue Obelisk, blogs, is @mhanwell on Twitter, and is active on Google+. He is passionate about open science, open source and making sense of increasingly large scientific data to understand the world around us.
He has played a key role in developing new development workflows as Kitware's open source projects moved to Git, working on Gerrit code review integration, running CDash@Home cloud-based testing with Gerrit code review and next generation build systems in the Titan, ITK, and VTK projects. He has also been awarded and led a Phase I and Phase II SBIR project to further develop open-source chemistry tools for computational chemistry, and has taken part in international collaborations to establish open standards for data exchange in chemistry.
Additionally, Marcus has been an active member of several open-source communities. He is one of the core developers of Avogadro, an open-source, 3D, cross-platform molecular visualization and editing application/library. He has been an active member of the Gentoo and KDE communities, and is a member of the KDE e.V. His work in Avogadro was featured by Trolltech on their "Qt in Use" pages, and he was selected as a Qt Ambassador. He won a Blue Obelisk award for his work in open chemistry, and continues to develop and promote open approaches in chemistry and related fields.

Christopher Jordan, Texas Advanced Computing Center (TACC)
Chris Jordan joined TACC in April 2008 to work on a variety of issues related to storage and I/O for high-performance computing, as well as long-term digital preservation issues. He currently leads the Data Management and Collections group, and is responsible for deploying research data infrastructure to serve the University of Texas System campuses and the national community. He has led data infrastructure activities for the National Science Foundation's TeraGrid and XSEDE projects. Before joining TACC, Chris spent four years at the San Diego Supercomputer Center, where he helped develop and deploy the GPFS-WAN global file system currently in production across multiple TeraGrid resource providers. He and his collaborators have published and spoken widely about the project. Chris has nearly ten years of experience working directly with some of the largest supercomputers and storage systems in the world, and has worked with a variety of architectures and scientific applications. His research interests include high performance, parallel I/O, digital preservation, scientific visualization and image rendering and non-traditional applications of high-performance computing.

Peter Murray-Rust, Cambridge
Peter Murray-Rust is now Reader in Molecular Informatics at the University of Cambridge and Senior Research Fellow of Churchill College.
His research in molecular informatics brings tools from computer science to chemistry, biosciences and earth sciences, integrating humans and machines in managing information. His research interests have involved the automated analysis of data in scientific publications, creation of virtual communities e.g. The Virtual School of Natural Sciences in the Globewide Network Academy and the Semantic Web. With Henry Rzepa he has extended this to chemistry through the development of Markup languages, especially Chemical Markup Language (CML), an expanding XML representation of molecular science including molecules, spectra, reactions, computational chemistry and solid state.
He campaigns for Open Data, particularly in science, and is on the advisory board of the Open Knowledge Foundation and a co-author of the Panton Principles for Open scientific data. Together with a few other chemists he was a founder member of the Blue Obelisk movement in 2005.
In 2002, Peter Murray-Rust and his colleagues proposed an electronic repository for unpublished chemical data called the World Wide Molecular Matrix (WWMM).
In 2011 he and Henry Rzepa were joint recipients of the Herman Skolnik Award of the American Chemical Society.

Neil Ostlund, Hypercube Inc.
In 1969, Ostlund received his Ph.D. degree from Carnegie Mellon University. As a professor of theoretical chemistry at the University of Arkansas, Ostlund took a sabbatical at Carnegie Mellon's computer science department and stayed for three years. In 1982, Ostlund then moved to the University of Waterloo, but as a professor of computer science, and the director of the computer architecture lab.
Ostlund started a molecular modeling company, Hypercube, in 1985 and eased out of his second tenured position by 1988. He says the move brought his career back into chemistry. "In computer science, I had to hide that I knew any chemistry," he says.
Ostlund now hires Ph.D. chemists "who pride themselves on becoming software engineers." Some of his employees have used his company as a transition out of chemistry into "pure" software careers. "They learn a lot of things training to the level of the Ph.D.: how to write, how to organize, how to be meticulous. It carries over to other professions." But in seeking capital for his business, the Ph.D. was not such an asset, he says. "If you're a chemist, you might have trouble convincing people that you are also a businessperson."

William Shelton, PNNL
Dr. William A. Shelton is the Associate Director of EMSL-the Environmental Molecular Sciences Laboratory. His primary responsibility is to lead the molecular sciences computing at EMSL in achieving its vision of integrating its full range of capabilities with computation including both numerical and data intensive computing. This will enable EMSL to reach its goal of being a premier scientific user facility for the Department of Energy by ensuring that EMSL develops and provides transformational computational and experimental resources along with recognized teams of researchers to provide a high level of expertise and collaboration to the scientific user community and conducts research that is focused on critical scientific issues.


The invited speakers will provide pedagogical and expository lectures on the methods that they use, complemented by hands-on sessions*. The format allows plenty of time for discussions.

Who: The workshop is open to the public. Travel support is available to participants from Grambling State University, Louisiana State University, Louisiana Tech University, Southern University at Baton Rouge, Tulane University, University of New Orleans, and Xavier University of Louisiana. (Depending on the number of applicants for travel support, students, postdocs, or staff may be required to share rooms.)

Where: 338 Johnston Hall, LSU campus: http://goo.gl/maps/Pla2B

Software, hardware, and background needed: Participants are expected to know basic linux, but they can be brought up to speed by taking the online courses "Intro to HPC", "Remote Access with SSH", and "Survival Skills with the BASH Shell" at https://docs.loni.org/moodle/.
*Participants need to bring their own laptop for the hands-on sessions, and will need to install software (TBA) prior to the workshop, if possible. If a participant does not have a laptop, he/she should let us know at the time of registration.

Registration: Registration is required. Late registration is accepted but preference will be given to those who register by June 1st. Registration fee is $50 to be used to cover snacks and two lunches. To register, visit the following link https://www.cct.lsu.edu/forms/sps-workshop .
LA-SiGMA members at LSU, LA Tech, and SUBR will later be reimbursed for this fee.

Lunch and refreshments will be provided each day. Participants cover their own transportation, and/or lodging costs. A limited number of travel awards are available to cover the travel expenses of qualified students or postdocs.

Parking: Persons utilizing a vehicle will need a LSU parking permit (Monday-Friday; no permits are needed Saturday and Sunday). You can get a visitor permit at the Visitor Center, Dalrymple Drive at Highland Road.

Lodging: We suggest staying at the Lod Cook Hotel located at LSU. You will need to reference LA-SiGMA in order to get the group rate of $93/night. This rate will be valid until June 1, or until the reserved block of rooms has been filled. A personal credit card must be presented at check-in.

Conference Organizers:
Juana Moreno, Louisiana State University, moreno AT lsu.edu
William Shelton, Pacific Northwest National Lab, William.Shelton AT pnnl.gov
Ramu Ramachandran, Louisiana Tech University, ramu AT latech.edu
Mark Jarrell, Louisiana State University, jarrellphysics -at- gmail.com

Other information:
About LSU: http://www.lsu.edu/visitors/images/thingstodo.pdf
About Baton Rouge: http://www.visitbatonrouge.com
LSU campus map: http://campusmap.lsu.edu/
LSU visitor parking map: https://sites01.lsu.edu/wp/parking/files/2011/08/VC_parking_map_FINAL-8_11_11.pdf

Sponsors:
The workshop is sponsored by the National Science Foundation EPSCoR Program and the Department of Energy, grant #EPS-1003897 and contract DE-AC05-76RLO1830, respectively.



This workshop is also made possible by the support of LA-SiGMA, the Center for Computation & Technology, the Environmental Molecular Sciences Laboratory of the Pacific Northwest National Laboratory (PNNL), and High Performance Computing at LSU.



For more information, please contact Shelley Lee at sjlee-at-cct.lsu.edu.