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http://www.google.com/sidewiki/intl/en/index.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 10, 2017. Sidewiki allows you to publish helpful information about any web page right in your browser, read insights in context from Sidewiki entries added by others, and share Sidewiki entries through Blogger, Facebook, Twitter and Google profiles. The toolbar with Sidewiki is free, installs in seconds and requires Internet Explorer 6+ or Firefox 2+; Windows XP SP2/Vista+. A Google Sidewiki extension is only available for Google Chrome 4.0+

Proper citation: Google Sidewiki (RRID:SCR_003206) Copy   

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http://www.qgene.org/

A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.

Proper citation: QGene (RRID:SCR_003209) Copy   

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http://compgen.bscb.cornell.edu/phast/

A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.

Proper citation: PHAST (RRID:SCR_003204) Copy   

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http://www.csir.res.in

Research and development organization that hosts a knowledgebase in diverse scientific areas. It also hosts a network of national Indian laboratories, outreach centres, and innovation complexes.

Proper citation: Council of Scientific and Industrial Research (RRID:SCR_003203) Copy   

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http://www.hologic.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 7, 2017. Formerly a commercial organization for clinical diagnostics, blood screening, transplant products and research products, it had been acquired by Hologic in 2012.

Proper citation: Gen-Probe (RRID:SCR_003202) Copy   

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https://github.com/hangelwen/miR-PREFeR

An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.

Proper citation: miR-PREFeR (RRID:SCR_003353) Copy   

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https://github.com/fhcrc/nestly

A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds.

Proper citation: Nestly (RRID:SCR_003472) Copy   

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http://cophs.mercer.edu/pharmsci.htm

The mission of the Department of Pharmaceutical Sciences is to make scholarly contributions to the discipline of pharmaceutical sciences and related fields. Education within the department offers a high quality learning environment that includes Ph.D. and Pharm.D./Ph.D. degree programs. Although not required for entry into pharmacy practice, a one-year residency is offered and affords the Pharm.D. graduate an opportunity to develop expertise in clinical pharmacy practice and specialty areas. The graduate program leading to the Ph.D. degree in pharmaceutical sciences is designed for students seeking teaching and research careers in academic institutions, the pharmaceutical industry and other health-related agencies. An interdisciplinary approach prepares graduates to perform independent research, to encourage scholarly development and to acquire teaching skills. Areas of specialization include pharmacology, pharmaceutics, toxicology, and medicinal chemistry. The Doctor of Pharmacy (Pharm.D.)/Doctor of Philosophy (Ph.D.) Degree Program enables highly qualified students to obtain both degrees in a shortened period of time. This Pharm.D./Ph.D. Degree program is designed primarily for students who are strongly motivated toward an academic/ research career in the pharmaceutical sciences. The Program is flexible enough to accommodate individuals of varied educational backgrounds.

Proper citation: Mercer University College of Pharmacy and Health Sciences; Department of Pharmaceutical Sciences (RRID:SCR_003479) Copy   

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http://departments.columbian.gwu.edu/psychology/graduate/cognitiveneuroscience

The Cognitive Neuroscience Program provides graduate students with an intense and focused research experience in the areas of perception, attention, and memory, with emphasis on the neural bases of these capacities. The program utilizes diverse research methods such as patient-based testing, neuro-imaging, animal modeling, and psychophysical scaling, and computational modeling. The goal of the program is to train students for careers in academic and research institutions. At the undergraduate level, the program provides both entry level and advanced courses as well as honor seminars in special topics. The program boasts a high faculty / student ratio, reflecting a strong emphasis on close collaboration between faculty and students on joint research projects. The Washington, DC research environment is outstanding, with the National Institutes of Health, Georgetown University, the University of Maryland, Johns Hopkins University, George Mason University, and other research institutions all close by. GWU's other resources for cognitive neuroscience research include a major medical school, a teaching hospital with world-class Neurology, Neurosurgery and Neuroradiology Departments, and an intensive Neuroscience Program. GWU is located in the heart of Washington, DC, a beautiful city with a wide variety of national museums, historical sites, restaurants, and cultural events. The Cognitive Neuroscience program at GW is designed to train students to become independent scientists who do basic research in an academic setting. Please note that ours is not a clinical neuropsychology program -- we provide no training in diagnosing or treating any brain or neurological disorder.

Proper citation: George Washington University, Cognitive Neuroscience (RRID:SCR_003356) Copy   

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http://www.mmc.edu/education/sogsr/academicprograms/phd_program/pharmacology/

Graduate Program in Pharmacology at Meharry Medical College embraces the broad definition of pharmacology as the study of how chemical agents affect living processes; the chemicals involved include agents such as endogenous hormones, neurotransmitters, and/or growth factors; toxic substances in our environment; and pharmaceutically developed drugs. The breadth of our scientific environment is manifested by faculty who study the fate of drugs once ingested and the variability of drug response in varying patient populations (a discipline known as pharmacokinetics), as well as faculty who study the mechanisms by which drugs and endogenous agents work (a discipline known as pharmacodynamics). A unique strength of our research and training environment is the inter-disciplinary nature of the program, which encompasses faculty from the four divisions of the Department of Biomedical Science and Departments of Internal Medicine and Neurology.

Proper citation: Meharry Medical College Pharmacology (RRID:SCR_003477) Copy   

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http://www.pictar.org

An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets

Proper citation: PicTar (RRID:SCR_003343) Copy   

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http://genome.ucsc.edu/cgi-bin/hgVisiGene

Virtual microscope for viewing in situ images that show where a gene is used in an organism, sometimes down to cellular resolution. The user can examine cell-by-cell as well as tissue-by-tissue expression patterns. Users can retrieve images that meet specific search criteria, then interactively zoom and scroll across the collection. Image set contributions are welcome. The following image collections are currently available for browsing: * High-quality high-resolution images of eight-week-old male mouse sagittal brain slices with reverse-complemented mRNA hybridization probes from the Allen Brain Atlas, courtesy of the Allen Institute for Brain Science * Mouse in situ images from the Jackson Lab Gene Expression Database (GXD) at MGI * Transcription factors in mouse embryos from the Mahoney Center for Neuro-Oncology * Mouse head and brain in situ images from NCBI''''s Gene Expression Nervous System Atlas (GENSAT) database * Xenopus laevis in situ images from the National Institute for Basic Biology (NIBB) XDB project

Proper citation: VisiGene Image Browser (RRID:SCR_003341) Copy   

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http://archive.gramene.org/plant_ontology/ontology_browse.html#to

A controlled vocabulary to describe phenotypic traits in plants. Each trait is a distinguishable feature, characteristic, quality or phenotypic feature of a developing or mature plant, or a plant part.

Proper citation: Plant Trait Ontology (RRID:SCR_003461) Copy   

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https://github.com/bgruening/galaxytools/tree/master/workflows/blockclust

Software for efficient clustering and classification of non-coding RNAs from short read RNA-seq profiles.

Proper citation: BlockClust (RRID:SCR_003347) Copy   

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http://www.montana.edu/cbn/

The academic programs and scientific research interests in our department cover a wide range of topics, with special emphasis on Cell Biology, Neurobiology, Developmental Biology, Physiology, Anatomy, Biophysics, and Neuroinformatics. Together, faculty and students in our department study biological processes that span the continuum from single cells to the entire human body. The Department of Cell Biology and Neuroscience offer both an Undergraduate and Graduate Program, which includes Ph.D. or M.S. degrees in Neuroscience or Biological Science. Two different undergraduate degree options are available within the Cell Biology and Neuroscience major: Biomedical Sciences and Cell Biology & Neuroscience. The Department of Cell Biology and Neuroscience offers exciting opportunities to work with nationally and internationally recognized faculty on a wide range of research topics, including cognitive neuroscience, neurophysiology, neuroinformatics, developmental biology, cell biology, biophysics and computational neuroscience.

Proper citation: Montana State University, Department of Cell Biology and Neuroscience (RRID:SCR_003467) Copy   

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http://www.utoledo.edu/med/depts/neurosciences/index.html

The Department of Neurosciences is highly committed to advancing the state of knowledge of nervous system structure and function through a tripartite mission of innovative research, state-of-the-art teaching methods, and dedicated service to the broader academic and surrounding communities. The teaching mission of our Department effectively communicates the current state of knowledge in neuroscience to the medical, graduate, and post-graduate students of the University using innovative methods. We are nationally known for using the most current technologies to teach human anatomy, embryology, and neurobiology to medical and graduate students. We teach critical thinking and problem solving skills and also provide opportunities for the students to excel in the laboratory and develop as life-long learners. Faculty participate in our Neurosciences and Neurological Disorders (NND) training track which awards both Ph.D. and M.S. degrees. We also train students towards the M.D./Ph.D and M.D./ M.S.B.S. joint degrees. Our research mission incorporates molecular, cellular, and systems neuroscience and cuts across the boundaries of traditional departments and disciplines. Our funded research in neurodevelopment, neurodegeneration, regeneration and repair, sensory function, and drug abuse comprise just a few of our interests. We employ cutting edge technologies and focus on the solution of fundamentally important problems pertinent to nervous system diseases and processes that can be translated feasibly to clinical issues. We work towards a synergistic interaction between the clinical and basic sciences that prompts unexpected discoveries of causes and novel treatments for the diseased nervous system. We also coordinate the Human Body Donation Program at the University of Toledo College of Medicine.

Proper citation: University of Toledo Health Sciences Campus; Neurosciences (RRID:SCR_003466) Copy   

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http://socialbrain.wordpress.com/2009/09/30/neurovia-download-neuro-imaging-tools-software-brain-project-matlab-program-package-for-the-analysis-of-functional-neuroimages/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on June 24, 2013. These distribution sets contain software modules and/or data sets extracted from the Visualization and Analysis Software Tools (VAST) library developed at the Minneapolis VA Medical Center, the University of Minnesota and/or the International Consortium for Neuroimaging (INC) (partially funded by the Human Brain Project )

Proper citation: Software Distribution Sets (RRID:SCR_003465) Copy   

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http://greallylab.einstein.yu.edu

It studies epigenetic regulation of the genome and its dysregulation in disease. This lab has a long-standing interest in gene regulatory processes that extend over large regions of the genome and give rise to human diseases. Our major projects are centred on the discovery of DNA sequence characteristics that discriminate genes undergoing genomic imprinting, using these to find new imprinted genes that are candidates for causing human disease.

Proper citation: Greally Lab (RRID:SCR_003339) Copy   

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http://www.drexelmed.edu/Home/AboutTheCollege/DepartmentsCentersandInstitutes/BasicScienceDepts/PharmacologyandPhysiology.aspx

The Department of Pharmacology and Physiology offers graduate programs leading to the M.S. and the Ph.D. degrees. The programs require independent research under the direction of departmental faculty members who are engaged in highly active research programs involving molecular, cellular, and behavioral approaches to experimental pharmacology and physiology in a strongly collaborative environment. The disciplines of pharmacology and physiology touch on virtually every scientific discipline and clinical area within the biomedical sciences, thereby providing students with a range of opportunities into disease mechanisms and altered physiological processes, new pharmacological tools and new medications. We are unique in offering educational programs not only in the basic sciences of pharmacology and physiology but also in drug discovery and development, which provides students with a wealth of advantages in considering career opportunities within academic, biopharmaceutical, and pharmaceutical settings. Students in both the PhD and MS programs begin their coursework with a core curriculum in biomedical sciences, and immediately start laboratory rotations. Intensive graduate-level pharmacology and physiology courses round out the core programmatic courses. Specialization in ion channel physiology, smooth-muscle physiology, neuropharmacology, behavioral pharmacology, and signal transduction processes may involve the taking of several elective courses. Each program requires the defense of a thesis based on original research. For more information visit, http://www.drexel.edu/catalog/g-about/pharm.htm.

Proper citation: Drexel University College of Medicine Pharmacology and Physiology (RRID:SCR_003338) Copy   

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http://neurobio.drexelmed.edu/

The Department of Neurobiology and Anatomy at the Drexel University College of Medicine provides an outstanding academic environment for pursuing multidisciplinary training and research in neuroscience. The department offers postdoctoral training through a NIH training grants and graduate student training through the Neuroscience program for outstanding individuals preparing for a research career in the biomedical sciences. The Department is also responsible for 3 major courses given to medical students that include Medical Neuroscience, Gross Anatomy and MicroAnatomy. Training can be obtained in all aspects of advanced microscopy and imaging, tissue culture, transplantation techniques, gene therapy and sequencing, behavioral neurobiology, kinematics, intracellular recording, patch clamping, computer modeling of neurobiological processes and robotics. The Department has well equipped shared facilities for confocal microscopy, electron microscopy, image acquisition and processing, small animal surgery, behavioral analysis, biochemistry and molecular biology. Research training is also supplemented by a seminar series featuring faculty, postdoctoral fellows and outside speakers. Journal clubs and discussions of research findings are scheduled regularly and often shared among individual laboratories.

Proper citation: Drexel University Neurobiology and Anatomy (RRID:SCR_003337) Copy   

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