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http://www.vetmed.lsu.edu/Summer_Scholars_Program.htm

The aim of the Summer Scholars Program is to provide veterinary medical students the opportunity to explore the world of biomedical research, develop and complete a biomedical research project during the summer. The intent is to engage students in a creative, problem-solving research activity and to provide a learning experience that will lead to the discovery of new knowledge in an area of their choosing and identify potential pathways to a career in biomedical research. Research plans will be developed by students with faculty mentor input, on any topic of interest to the student and likely to lead to the discovery of new information. Example topics are: immunology and infectious diseases, cancer biology, molecular epidemiology, experimental studies focused on nutrition and obesity, pharmacology, environmental toxicology, mechanisms of pathogenesis, zoonoses, biomechanics, cardiovascular pathophysiology, and others. The mentor and other advisors will provide guidance to students and an assessment of progress. Students will provide at completion of the study, an oral presentation of their results to their colleagues and all mentors and a presentation of results via posters at the annual Merial NIH National Veterinary Scholars Symposium, to be held in 2010 at the University of Georgia, and at the LSU Phi Zeta Research Emphasis Day. It is noteworthy that one Summer Scholar won an award at the 2008 LSU Phi Zeta Research Emphasis Day. LSU Students will receive elective credit in the curriculum (VMED 5010 or VMED 5463) for successful completion of the program. Students will be strongly encouraged to work with their mentors to publish their findings in peer-reviewed journals separately or as a smaller piece of work with their mentors. Sponsors: The program is funded by a Merial Foundation grant and an NIH T35 training grant.

Proper citation: Merial/NIH Veterinary Scholars Program (RRID:SCR_008301) Copy   

•   Source: SciCrunch Registry

http://www.vetmed.wisc.edu/ms-phd/

The Comparative Biomedical Sciences Graduate Degree program provides exceptional graduate research training in core areas of animal and human health including genomics, immunology, molecular and cellular biology, physiology, infectious disease, neuroscience, pharmacology and toxicology, and oncology. Seventy-five faculty members in a diverse number of UW departments including Bacteriology, Biochemistry, Medical Microbiology and Immunology, Medicine, Oncology, Pathology, Radiology in addition to the 4 departments of the School of Veterinary Medicine are trainers in the program. These internationally recognized professors, as well as the integrative nature of our program, provide outstanding and unique research opportunities for our students. Because the University of Wisconsin is consistently ranked as one of the best 10 graduate institutions in the nation, the strength of our program is not only due to the superb research and teaching of our faculty but also due to the University as a whole. Approximately 55 students, most of whom are Ph.D. candidates, are currently enrolled in the program. Research strategies and academic curricula are tailored to the specific needs of each individual student. Graduates from our program are highly successful in the biotechnology industry and at top-ranked research institutions in the U.S. and abroad. The Comparative Biomedical Sciences Graduate Program offers a diverse number of research opportunities in multiple fields of study. A brief description of some of the major areas of research being performed by faculty affiliated with the Comparative Biomedical Sciences Graduate Program is provided below. Use the pull down menu above or click on the heading to find faculty members doing research in these areas. Sponsors: CBMS is supported by the University of Wisconsin

Proper citation: Comparative Biomedical Sciences Graduate Program (RRID:SCR_008304) Copy   

•   Source: SciCrunch Registry

http://code.google.com/

Developer tools, APIs and resources. Search developers.google.com and code.google.com.

Proper citation: Google Code (RRID:SCR_005786) Copy   

•   Source: SciCrunch Registry

http://collaborations.gis.a-star.edu.sg/~cmb6/TherMos/

Software used for estimating protein-DNA binding energies from in vivo binding profiles. It is a de novo motif discovery algorithm that exploits the information in transcription factor ChIP-seq or ChIP-exo datasets based on a more natural thermodynamic formalism., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: TherMos (RRID:SCR_002790) Copy   

•   Source: SciCrunch Registry

http://www.well.ox.ac.uk/platypus

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 16,2023. Software tool designed for efficient and accurate variant detection in high throughput sequencing data. Haplotype based variant caller for next generation sequence data.

Proper citation: Platypus (RRID:SCR_005389) Copy   

•   Source: SciCrunch Registry

https://mzmatch.sourceforge.net/MetAssign.php

Software that combines information from the mass-to-charge ratio, retention time and intensity of each peak, together with a model of the inter-peak dependency structure, to increase the accuracy of peak annotation. The software has been implemented as part of the mzMatch metabolomics analysis pipeline, which is available for download.

Proper citation: MetAssign (RRID:SCR_000092) Copy   

•   Source: SciCrunch Registry

https://www.pgscatalog.org/

Open database of polygenic scores and relevant metadata required for accurate application and evaluation. Used for reproducibility and systematic evaluation.

Proper citation: Polygenic Score Catalog (RRID:SCR_023558) Copy   

•   Source: SciCrunch Registry

https://cdip.ucsd.edu/

Network for monitoring waves and beaches and prediction of waves and shoreline change along coastlines of United States. Since 1975 program has produced database of publicly accessible environmental data for use by coastal engineers and planners, scientists, mariners, and marine enthusiasts. Forefront of coastal monitoring, developing numerous innovations in instrumentation, system control and management, computer hardware and software, field equipment, and installation techniques. Operated by Ocean Engineering Research Group, part of Integrative Oceanography Division at Scripps Institution of Oceanography. CDIP measures, analyzes, archives and disseminates coastal environment data for use by coastal engineers, planners and managers, as well as scientists and mariners.

Proper citation: Coastal Data Information Program (RRID:SCR_024649) Copy   

•   Source: SciCrunch Registry

https://open.oncobox.com/

Structured curated collection of protein based and of metabolic human molecular pathways. Human molecular pathways database with tools for activity calculating and visualization.All pathways are functionally classified according to GO terms enrichment patterns. All pathway participants, their interactions and reactions are uniformly processed and annotated, and are ready for numeric analysis of experimental expression data.For every comparison graph is generated summarizing top up and down regulated pathways.

Proper citation: OncoboxPD (RRID:SCR_023723) Copy   

•   Source: SciCrunch Registry

http://wpicr.wpic.pitt.edu/WPICCompGen/

Software application (entry from Genetic Analysis Software)

Proper citation: R/SPECTRAL-GEM (RRID:SCR_007414) Copy   

•   Source: SciCrunch Registry

https://kanphos.neuroinf.jp/

Database system that provides phosphorylated sites and information about which substrates are phosphorylated by specific kinase and which extracellular stimuli activate or inhibit protein phosphorylation via intracellular signaling cascades.

Proper citation: Kinase Associated Neural Phospho Signaling (RRID:SCR_023659) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/nondetects.html

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

http://mouse.cs.ucla.edu/emma/

Statistical test for model organisms association mapping correcting for the confounding from population structure and genetic relatedness. EMMA takes advantage of the specific nature of the optimization problem in applying mixed models for association mapping, which substantially increases the computational speed and the reliability of the results. The current implementation of EMMA is available in an R package. The documentation is included in the installation package.

Proper citation: Efficient Mixed-Model Association (RRID:SCR_008217) Copy   

•   Source: SciCrunch Registry

http://www.openbioinformatics.org/

An open bioinformatis software repository with no tie to any organization or institution. Contact them to host your software.

Proper citation: OpenBioinformatics.org (RRID:SCR_002229) Copy   

•   Source: SciCrunch Registry

https://neurophysics.ucsd.edu/software.php

Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. This sofwtare was developed by the David Kleinfeld Laboratory at UC San Diego.

Proper citation: UltraMegaSort 2000 (RRID:SCR_015857) Copy   

•   Source: SciCrunch Registry

https://github.com/emsweene/SuBLIME_package

Software used for detection of lesions in patients with multiple sclerosis. It provides an automated method for segmenting incident lesion voxels and allows for sensitive and specific detection of lesion incidence that can be applied to large collections of images. Using the explicit form of the statistical model, SuBLIME can be adapted to cases when more or fewer imaging sequences are available.

Proper citation: SuBLIME (RRID:SCR_014409) Copy   

•   Source: SciCrunch Registry

https://michaelbach.de/fract/index.html

Software tool for visual test battery in form of a free computer program.Can be run within your browser or download as a stand-alone program. Used by many vision labs, optometrists and ophthalmologists.

Proper citation: Freiburg Vision Test ('FrACT') (RRID:SCR_016439) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/icacompass/

Algorithm for MATLAB and the EEGLAB toolbox that enables the automatic detection of independent components from an ICA that represent event-related brain potentials. It performs automatic Independent Component (IC) selection with respect to the contributions of the ICs to a certain ERP.

Proper citation: COMPASS (RRID:SCR_015874) Copy   

•   Source: SciCrunch Registry

http://gps.biocuckoo.org/

Software that detects kinase-specific phosphorylation sites. GPS provides a platform able to perform its prediction based on a group-based phosphorylation scoring algorithm. It allows users to query multiple protein sequences through a batch prediction mode.

Proper citation: GPS (RRID:SCR_016374) Copy   

•   Source: SciCrunch Registry

http://www.sanger.ac.uk/science/tools/alien-hunter

Software for the prediction of putative Horizontal Gene Transfer (HGT) events with the implementation of Interpolated Variable Order Motifs (IVOMs). The predictions (embl format) can be automatically loaded into Artemis genome viewer.

Proper citation: Alien-hunter (RRID:SCR_015967) Copy   

•   Source: SciCrunch Registry