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http://www.brainline.org/

BrainLine is a national multimedia project offering information and resources about preventing, treating, and living with TBI. BrainLine includes a series of webcasts, an electronic newsletter, and an extensive outreach campaign in partnership with national organizations concerned about traumatic brain injury. BrainLine serves anyone whose life has been affected by TBI. That includes people with brain injury, their families, professionals in the field, and anyone else in a position to help prevent or ameliorate the toll of TBI. Through BrainLine, we seek to provide a sense of community, a place where people who care about TBI can go 24 hours a day for information, support, and ideas. BrainLine is funded by the Defense and Veterans Brain Injury Center, the Primary Operational TBI Component of the Defense Centers of Excellence for Psychological Health and Traumatic Brain Injury, through a subcontract award with the Henry M. Jackson Foundation for the Advancement of Military Medicine.

Proper citation: BrainLine (RRID:SCR_006603) Copy   

•   Source: SciCrunch Registry

http://cytoseg.googlecode.com

A tool for automatic segmentation of 3D biological datasets, with emphasis on 3D electron microscopy. It works best for 3D blob shaped objects like mitochondria, lysosomes, etc. The project is written in Python and uses the pythonxy platform (which includes scipy and ITK image processing tools).

Proper citation: Cytoseg (RRID:SCR_009553) Copy   

•   Source: SciCrunch Registry

http://www.math.mcgill.ca/keith/surfstat

A Matlab toolbox for the statistical analysis of univariate and multivariate surface data using linear mixed effects models and random field theory.

Proper citation: SurfStat (RRID:SCR_007081) Copy   

•   Source: SciCrunch Registry

http://iczn.org/

An organization that acts as adviser and arbiter for the zoological community by generating and disseminating information on the correct use of the scientific names of animals. The ICZN is responsible for producing the International Code of Zoological Nomenclature - a set of rules for the naming of animals and the resolution of nomenclatural problems.

Proper citation: ICZN (RRID:SCR_010241) Copy   

•   Source: SciCrunch Registry

http://www.armystarrs.org/

Study of mental health risk and resilience factors ever conducted among military personnel. The purpose of Army STARRS is to identify as quickly as possible factors that protect or pose risks to Soldiers'' emotional well-being and overall mental health so that the Army may apply the knowledge to its ongoing health promotion, risk reduction, and suicide prevention efforts. Army STARRS investigators will use four separate study components the Historical Data Study, New Soldier Study, All Army Study, and Soldier Health Outcomes Study to identify factors that help protect a Soldier''s mental health and factors that put a Soldier''s mental health at risk. Army STARRS is a five-year study that will run through 2014. Findings will be reported as they become available, so that the Army may apply them to its ongoing health promotion, risk reduction, and suicide prevention efforts. Given its length and scope, Army STARRS will generate a vast amount of information and will allow investigators to focus on periods in a military career that are known to be high risk for psychological problems. The information gathered from volunteer participants throughout the study will help researchers identify not only potentially relevant risk factors, but potential protective factors as well. Because promoting mental health and reducing suicide risk are important for all Americans, the findings from Army STARRS will benefit not only servicemembers but the nation as a whole. NIMH has assembled a group of renowned experts to carry out this research including teams from the Uniformed Services University of the Health Sciences (USUHS), the University of California, San Diego, University of Michigan, Harvard Medical School, and NIMH. Additional Army and NIMH program staff will contribute to the oversight and implementation of the study. This research team brings together international leaders in military health, health and behavior surveys, epidemiology, suicide, and genetic and neurobiological factors involved in psychological health.

Proper citation: Army STARRS (RRID:SCR_006708) Copy   

•   Source: SciCrunch Registry

https://medicine.missouri.edu/departments/medical-pharmacology-and-physiology

The Department of Medical Pharmacology and Physiology has been known for outstanding programs in exercise physiology and cardiovascular physiology. The Department offers both Master of Science (MS) and Doctor of Philosophy (PhD) degree programs that provide students with excellent preparation for a variety of challenging and rewarding careers. The degrees offered are programs in Pharmacology or Physiology. The Medical Pharmacology and Physiology Department and its modern research and teaching facilities are on campus in the School of Medicine. The research laboratories of the faculty have excellent equipment and maintenance support. The award-winning Health Sciences Library, containing a wide variety of current journals and resource books, is located in the School of Medicine. Modern student computer stations are also available. Animal quarters and animal care are under the direction of qualified veterinarians. Other important University facilities include a nuclear reactor for providing short-lived radioisotopes and a campus-wide computer network. The Center for Gender Physiology manages four core facilities that provide animal models, equipment and expertise required to explore gender differences in physiological function.

Proper citation: University of Missouri Department of Medical Pharmacology and Physiology (RRID:SCR_007518) Copy   

•   Source: SciCrunch Registry

http://research.mssm.edu/cnic/

Center to advance research and training in mathematical, computational and modern imaging approaches to understanding the brain and its functions. Software tools and associated reconstruction data produced in the center are available. Researchers study the relationships between neural function and structure at levels ranging from the molecular and cellular, through network organization of the brain. This involves the development of new computational and analytic tools for imaging and visualization of 3-D neural morphology, from the gross topologic characteristics of the dendritic arbor to the fine structure of spines and their synapses. Numerical simulations of neural mechanisms based on these structural data are compared with in-vivo and in-vitro electrophysiological recordings. The group also develops new theoretical and analytic approaches to exploring the function of neural models of working memory. The goal of this analytic work is to combine biophysically realistic models and simulations with reduced mathematical models that capture essential dynamical behaviors while reproducing the functionally important features of experimental data. Research areas include: Imaging Studies, Volume Integration, Visualization Techniques, Medial Axis Extraction, Spine Detection and Classification, Applications of Rayburst, Analysis of Spatially Complex Structures, Computational Modeling, Mathematical and Analytic Studies

Proper citation: Computational Neurobiology and Imaging Center (RRID:SCR_013317) Copy   

•   Source: SciCrunch Registry

http://gwyddion.net/

Modular program for SPM (scanning probe microscopy) data visualization and analysis. Primarily it is intended for the analysis of height fields obtained by scanning probe microscopy techniques (AFM, MFM, STM, SNOM/NSOM) and it supports a lot of SPM data formats. However, it can be used for general height field and (greyscale) image processing, for instance for the analysis of profilometry data or thickness maps from imaging spectrophotometry.

Proper citation: Gwyddion (RRID:SCR_015583) Copy   

•   Source: SciCrunch Registry

https://web.njit.edu/~matveev/calc.html

A modeling tool for simulating intracellular calcium diffusion and buffering. CalC solves continuous reaction-diffusion PDEs describing the entry of calcium into a volume through point-like channels, and its diffusion, buffering and binding to calcium receptors. Its features include: being platform-independent; being operated by simple script; combinable with MATLAB; and providing real-time views. Demos and manuals are provided on the website.

Proper citation: CalC (RRID:SCR_014259) Copy   

•   Source: SciCrunch Registry

https://www.mcgill.ca/bic/resources/omega

Open data repository fully dedicated to MEG data in raw and processed form. The archive also contains anatomical MRI volumes and demographic and questionnaire information. Organized and stored as the Brain Imaging Data Structure (BIDS) with the integration of multimodal electrophysiology data. Directly readable by data-analysis software with Brainstorm. OMEGA will continue to expand, with contributions from the scientific community.

Proper citation: Open MEG Archive (RRID:SCR_014930) Copy   

•   Source: SciCrunch Registry

http://www.novocraft.com/products/novoalign/

Software tool designed for mapping short reads onto a reference genome generated from Illumina, Ion Torrent, and 454 NGS platforms. Its features include paired end alignment, methylation status analysis, automatic base quality calibration, and in built adapter trimming and base quality trimming.

Proper citation: NovoAlign (RRID:SCR_014818) Copy   

•   Source: SciCrunch Registry

https://evidencemodeler.github.io/

Software tool for automated eukaryotic gene structure annotation that reports eukaryotic gene structures as weighted consensus of all available evidence. Used to combine ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. Inputs include genome sequence, gene predictions, and alignment data (in GFF3 format).

Proper citation: EVidenceModeler (RRID:SCR_014659) Copy   

•   Source: SciCrunch Registry

http://pasapipeline.github.io/

Gene structure annotation and analysis tool that uses spliced alignments of expressed transcript sequences to automatically model gene structures. It also incorporates gene structures based on transcript alignments into existing gene structure annotations. It is one component of a larger eukayotic annotation pipeline implemented at the Broad Institute.

Proper citation: PASA (RRID:SCR_014656) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://iidp.coh.org/Default.aspx

The goal of the Integrated Islet Distribution Program (IIDP) is to work with the leading islet isolation centers in the U.S. to distribute high quality human islets to the diabetes research community, in order to advance scientific discoveries and translational medicine.

Proper citation: Integrated Islet Distribution Program (IIDP) (RRID:SCR_014387) Copy   

•   Source: SciCrunch Registry

http://www.mathworks.com/help/fuzzy/index.html

A software toolbox which provides MATLAB functions, apps, and a Simulink block for analyzing, designing, and simulating fuzzy logic systems. Fuzzy Logic Toolbox allows users to model complex system behaviors using simple logic rules, and then implement these rules in a user-designed fuzzy inference system. Functions are provided for many common methods, including fuzzy clustering and adaptive neurofuzzy learning. The toolbox can be used as a stand-alone fuzzy inference engine or in connection with Simulink. Different versions of the software are available for specific fuzzy inference systems.

Proper citation: Fuzzy Logic Toolbox (RRID:SCR_014268) Copy   

•   Source: SciCrunch Registry

https://github.com/nbcrrolls/workflows/tree/master/Production/AmberGPUMDSimulation

A workflow for running molecular dynamics simulations. It can be used for all-atom molecular dynamic simulations, which involve five steps of minimization, one step of heating, three steps of equilibration, and one or more instances of production. The input is a set of directories that include the MD simulation input scripts, system topology and coordinate files. Output files are list of plots, simulation trajectories, intermediate files, restart files, and the like.

Proper citation: Molecular Dynamics Workflow (BioKepler) (RRID:SCR_014389) Copy   

•   Source: SciCrunch Registry

https://code.google.com/archive/p/edlut/

Simulation software which creates spiking cell models using either a time-driven strategy or an event-driven strategy based on look-up tables. EDLUT serves as a tool for studying the computational principles of neural systems to reveal how different functionalities of the brain and central nervous system are based on cell and topology properties.

Proper citation: EDLUT (RRID:SCR_014261) Copy   

•   Source: SciCrunch Registry

https://biotium.com/

An Antibody supplier

Proper citation: Biotium inc (RRID:SCR_013538) Copy   

•   Source: SciCrunch Registry

http://search.cpan.org/dist/Bio-ToolBox/lib/Bio/ToolBox.pm

Tools for querying and analysis of genomic data. These libraries provide a useful interface for working with bioinformatic data. Many bioinformatic data analysis revolves around working with tables of information, including lists of genomic annotation (genes, promoters, etc.) or defined regions of interest (epigenetic enrichment, transcription factor binding sites, etc.). This library works with these tables and provides a set of common tools for working with them. Opening and saving common tab-delimited text formats Support for BED, GFF, VCF, narrowPeak files Scoring intervals with datasets from microarray and sequencing ChIPSeq, RNASeq, microarray expression Support for Bam, BigWig, BigBed, wig, and USeq data formats Intersection with other known annotation Works with any genomic annotation in GTF, GFF3, and UCSC formats The libraries provide a unified and integrated approach to analyses. In many cases, they provide an abstraction layer over a variety of different specialized BioPerl and related modules. Instead of writing numerous scripts specialized for each data format (wig, bigWig, Bam), one script can now work with any data format.

Proper citation: BioToolBox (RRID:SCR_015696) Copy   

•   Source: SciCrunch Registry

http://www.aniseed.cnrs.fr/

Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata.
This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories.
ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website.

Proper citation: Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) Copy   

•   Source: SciCrunch Registry