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Funding Update: NSF Bioinformatics Grants Awarded June 12 — July 9, 2012

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Galaxy-P: A new community-based informatics paradigm for MS-based proteomics
Start Date: July 15, 2012
Expires: June 30, 2015
Awarded Amount to Date: $457,548
Principal Investigator: Timothy Griffin
Sponsor: University of Minnesota, Twin Cities

The funds will be used to extend the Galaxy framework by integrating a series of software programs into tool modules for mass spectrometry-based proteomics data analysis, which will be referred to as Galaxy-P.


An integrated approach for computationally designing and experimentally characterizing fully-human antibodies
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $194,709
Principal Investigators: Costas Maranas, Thomas Wood
Sponsor: Pennsylvania State University, University Park

Supports the development of a “combinatorial database of all germline antibody variable domain structures encoded in the human genome.” The database will be used to develop a computational tool — dubbed Optimal Method for Antibody Variable region Engineering — for designing human antibodies against specified antigens and antibody libraries, which will be used to test the “effectiveness of computations to drive antibody design.”


PathBubbles for dynamic visualization and integration of biological information
Start Date: July 1, 2012
Expires: June 30, 2015
This grant is awarded to three investigative teams:
Carl Schmidt, Vijay Shanker, Cecilia Arighi; University of Delaware; $194,709
Fiona McCarthy; Mississippi State University; $218,690
Jian Chen; University of Southern Mississippi; $394,007

Supports the development of PathBubbles — an interactive pathway visualization tool that uses the Vis- and Code Bubbles as a framework. The investigators will also integrate data found in specific ontologies, text mining tools, and expression data to provide gene annotation for use with PathBubbles. They will also include functional information from scientific literature about post-translationally modified proteins which is expected to assist users in developing testable hypotheses.


Exploring taxon concepts through analyzing fine-grained semantic markup of descriptive literature
Start Date: July 1, 2012
Expires: June 30, 2016
This grant is awarded to two investigative teams:
Hong Cui, James Macklin; University of Arizona; $1,095,682
Bertram Ludaescher; University of California, Davis; $392,114

The funds will support the development of novel ways to tie scientific names directly to published biological characteristics of organisms as well as to implement a new program dubbed the Explorer of Taxon Concepts which will assist with “the disambiguation of the scientific names of species at all taxonomic ranks.” According to the abstract, the ETC program will enable “text-mining extraction of taxonomic knowledge from scientific literature; analysis and integration of this knowledge using logic-based reasoning and information theoretic methods; and result visualization.”


A flexible platform for accelerating biological sequence analysis
Start Date: July 1, 2012
Expires: June 30, 2013
Awarded Amount to Date: $99,653
Principal Investigators: Jeremy Buhler, Mark Franklin, Roger Chamberlain
Sponsor: Washington University

Supports the development of infrastructure for accelerated biological sequence analysis applications. According to the abstract, the investigators will design criteria for a hardware platform and software tools that will speed the “creation, validation, and deployment of biosequence accelerators.” As part of these efforts the researchers will qualify hardware platforms, develop prototype software and firmware, and consult developer and user communities for accelerated sequence analysis tools to guide the planning effort, the abstract states.


A synthetic biology design-build-test platform for automated combinatorial DNA Assembly
Start Date: July 1, 2012
Expires: Dec. 31, 2012
Awarded Amount to Date: $150,000
Principal Investigator: Michael Fero
Sponsor: TeselaGen

The funds will support the development of software comprised of a “screening and functional testing system for synthetic biology.” According to the abstract, the investigators will develop a tool that will help with the “construction of complex DNA assemblies and combinatorial libraries” and allow scientists to “direct their resources to conducting experiments that address primary issues.”


Error Correction for Biomolecular Computations
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $449,998
Principal Investigator: John Reif
Sponsor: Duke University

The funds will support the development of methods for “error-correction of leaks” in DNA computations by developing “network level designs and gate level designs that suppress leaks” using things like “shadow networks and error-modulation gates.”


Genetic design automation
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $449,990
Principal Investigator: Chris Myers
Sponsor: University of Utah

The funds will support the development of a genetic design automation tools to support the analysis and design of synthetic genetic circuits. According to the abstract, these tools will leverage standards such as the Systems Biology Markup Language and Synthetic Biology Open Language so that the models and designs can be exchanged. Furthermore, the investigators intend to develop new modeling, analysis, and visualization methods that will enable users to study the behavior of bacterial populations.


Algorithms for accurate prediction of protein interaction sites by integrating sequence, structure, and network data
Start Date: July 1, 2012
Expires: June 30, 2015
Awarded Amount to Date: $420,000
Principal Investigator: Yu Xia
Sponsor: Trustees of Boston University

These funds will support the development of computational algorithms that will use publicly available protein sequence, structure, and network data to predict amino acid sites that mediate protein interactions. Specifically, the investigators intend to develop two algorithms which will be able to identify amino acid residues on the surface of proteins “that evolve more slowly than expected” and short sequence motifs “that are enriched among non-homologous proteins with a common interacting partner” both of which are “strong candidates” for mediating protein interactions.


PlantSimLab: A simulation laboratory for plant biology
Start Date: June 15, 2012
Expires: May 31, 2015
Awarded Amount to Date: $881,510
Principal Investigators: Reinhard Laubenbacher, Brett Tyler, John McDowell, Stefan Hoops
Sponsor: Virginia Polytechnic Institute and State University

These funds will support the development of network modeling tool dubbed PlantSimLab that will enable plant biologists to build, validate, and use computer models.


How do phage drive bacterial diversity in Lake Michigan near-shore waters? A bioinformatics perspective
Start Date: June 15, 2012
Expires: May 31, 2017
Awarded Amount to Date: $281,823
Principal Investigator: Catherine Putonti
Sponsor: Loyola University of Chicago

According to the abstract, the funds will be used to establish a team that will develop and apply new tools for the synthesis of next-generation viral metagenomic sequence data.


Development and application of graphical user interfaces for systems building and analysis of membrane simulations
Start Date: June 1, 2012
Expires: May 31, 2015
This grant is awarded to two investigative teams:
Wonpil Im; University of Kansas Center for Research; $109,149
Jeffery Klauda; University of Maryland, College Park; $40, 070

The funds will support the development of graphical user interfaces that will allow researchers to setup, perform, and analyze various member simulations. According to the abstract, the GUI’s will be based on the Membrane Builder software in CHARMM-GUI and will let users analyze membrane simulation trajectories from simulation programs including CHARMM, Amber, GROMACS, and NAMD. As part of the project, the investigators will further develop Membrane Builder so that it includes more lipid molecules; tools to build monolayer, micelle, and vesicle systems; and provide simulation inputs for GROMACS and Amber packages.


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