Tools   Select Another Resource Report Type

https://reich.hms.harvard.edu/software

Software application that finds skews in ancestry that are potentially associated with disease genes in recently mixed populations like African Americans. It can be downloaded for either UNIX or Linux.

Proper citation: Ancestrymap (RRID:SCR_004353) Copy   

•   Source: SciCrunch Registry

http://cmrm.med.jhmi.edu/cmrm/atlas/human_data/file/JHUtemplate_newuser.html

DTI white matter atlases with different data sources and different image processing. These include single-subject, group-averaged, B0 correction, processed atlases (White Matter Parcellation Map, Tract-probability maps, Conceptual difference between the WMPM and tract-probability maps), and linear or non-linear transformation for automated white matter segmentation. # Adam single-subject white matter atlas (old version): These are electronic versions of atlases published in Wakana et al, Radiology, 230, 77-87 (2004) and MRI Atlas of Human White Matter, Elsevier. ## Original Adam Atlas: 256 x 256 x 55 (FOV = 246 x 246 mm / 2.2 mm slices) (The original matrix is 96x96x55 (2.2 mm isotropic) which is zerofilled to 256 x 256 ## Re-sliced Adam Atlas: 246 x 246 x 121 (1 mm isotropic) ## Talairach Adam: 246 x 246 x 121 (1 mm isotropic) # New Eve single-subject white matter atlas: The new version of the single-subject white matter atlas with comprehensive white matter parcellation. ## MNI coordinate: 181 x 217 x 181 (1 mm isotropic) ## Talairach coordinate: 181 x 217 x 181 (1 mm isotropic) # Group-averaged atlases: This atlas was created from their normal DTI database (n = 28). The template was MNI-ICBM-152 and the data from the normal subjects were normalized by affine transformation. Image dimensions are 181x217x181, 1 mm isotropic. There are two types of maps. The first one is the averaged tensor map and the second one is probabilistic maps of 11 white matter tracts reconstructed by FACT. # ICBM Group-averaged atlases: This atlas was created from ICBM database. All templates follow Radiology convention. You may need to flip right and left when you use image registration software that follows the Neurology convention.

Proper citation: DTI White Matter Atlas (RRID:SCR_005279) Copy   

•   Source: SciCrunch Registry

http://www.dartmouth.edu/~rswenson/Atlas/

On line labeled atlas of the human brain developed by Dr. Rand Swenson of Dartmouth Medical School. It includes gross anatomical and MRI-generated slices (Axial T1-weighted MRI and Coronal T2 MRI weighted, along with Magnetic resonance arteriogram (MRA) and Magnetic resonance venogram (MRV)images. Labels may be turned on and off. A companion on-line textbook is also available. The site says it is still under construction, although the copyright is 2009. * Atlas of Gross Brain Topography * Atlas of the Brain Stem in Cross Section * Atlas of the Brain in Axial Slices * Atlas of the Brain in Coronal Slices * Atlas of the Head in Axial Slices * Axial T1-weighted MRI * Axial T2-weighted MRI * Coronal T1 MRI * Coronal T2 MRI * Magnetic resonance arteriogram (MRA) * Magnetic resonance venogram (MRV)

Proper citation: Atlas of the Brain (RRID:SCR_005967) Copy   

•   Source: SciCrunch Registry

http://www.civm.duhs.duke.edu/neuro2012ratatlas/

Multidimensional atlas of the adult Wistar rat brain based on magnetic resonance histology (MRH). The atlas has been carefully aligned with the widely used Paxinos-Watson atlas based on optical sections to allow comparisons between histochemical and immuno-marker data, and the use of the Paxinos-Watson abbreviation set. Our MR atlas attempts to make a seamless connection with the advantageous features of the Paxinos-Watson atlas, and to extend the utility of the data through the unique capabilities of MR histology: a) ability to view the brain in the skull with limited distortion from shrinkage or sectioning; b) isotropic spatial resolution, which permits sectioning along any arbitrary axis without loss of detail; c) three-dimensional (3D) images preserving spatial relationships; and d) widely varied contrast dependent on the unique properties of water protons. 3D diffusion tensor images (DTI) at what we believe to be the highest resolution ever attained in the rat provide unique insight into white matter structures and connectivity. The 3D isotropic data allow registration of multiple data sets into a common reference space to provide average atlases not possible with conventional histology. The resulting multidimensional atlas that combines Paxinos-Watson with multidimensional MRH images from multiple specimens provides a new, comprehensive view of the neuroanatomy of the rat and offers a collaborative platform for future rat brain studies. To access the atlas, click view supplementary materials in CIVMSpace at the bottom of the following webpage.

Proper citation: Adult Wistar Rat Atlas (RRID:SCR_006288) Copy   

•   Source: SciCrunch Registry

http://www003.upp.so-net.ne.jp/pub/publications.html#sl

Software application for inkage disequilibrium grouping of single nucleotide polymorphisms (SNPs) reflecting haplotype phylogeny for efficient selection of tag SNPs. (entry from Genetic Analysis Software)

Proper citation: LDGROUP (RRID:SCR_006282) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/Gsnap2Augustus

Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap.

Proper citation: Gsnap2Augustus (RRID:SCR_017555) Copy   

•   Source: SciCrunch Registry

http://hub.docker.com/r/marchalc/hicres/

Software pipeline to estimate and predict genomic resolution of Hi-C libraries. Used for estimating and predicting HiC library resolution.

Proper citation: HiCRes (RRID:SCR_022319) Copy   

•   Source: SciCrunch Registry

https://huttenhower.sph.harvard.edu/picrust/

Software for predicting functional abundances based only on marker gene sequences.Used for prediction of metagenome functions. Contains updated and larger database of gene families and reference genomes, provides interoperability with any operational taxonomic unit (OTU)-picking or denoising algorithm, and enables phenotype predictions. Allows addition of custom reference databases.

Proper citation: PICRUSt2 (RRID:SCR_022647) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/NCBITAXON

Ontology that is an automatic translation of the NCBI taxonomy (a taxonomic classification of living organisms and associated artifacts) database into obo/owl.

Proper citation: NCBITaxon (RRID:SCR_000479) Copy   

•   Source: SciCrunch Registry

https://cytotrace.stanford.edu/

Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.

Proper citation: CytoTRACE (RRID:SCR_022828) Copy   

•   Source: SciCrunch Registry

http://www.ohsu.edu/xd/education/schools/school-of-medicine/academic-programs/neuroscience-graduate-program//

The Neuroscience Graduate Program (NGP) at OHSU provides outstanding, multidisciplinary training in neuroscience in one of the best-recognized neuroscience programs in the United States. Our graduates are distributed at top research institutions throughout the world, and the success of our faculty ensures that graduates have ready access to their next step ����?? be it postdoctoral fellowships in academia or industry, or other science-related careers. The program is particularly strong in cellular neuroscience, neuronal signaling, gene regulation, biophysics of channels and transporters, sensory systems, and neuroendocrinology with increasing strength in developmental neuroscience and disease-oriented neuroscience research. Faculty members are located within research institutes at OHSU including the Vollum Institute, the Oregon National Primate Research Center (ONPRC), Oregon Hearing Research Center, Jungers Center and the Center for Research on Occupational and Environmental Toxicology (CROET); as well as the basic and clinical departments in the OHSU School of Medicine. As time spent in the lab is the most important component of graduate science training, our program is designed such that core coursework is completed in the first year. During that first year, students also are immersed in research through lab rotations in several labs, eventually choosing one that gives a mutual fit. Because of the relatively small number of students compared to the number of neuroscience laboratories at OHSU, students have many options for a thesis lab. Our well funded faculty provide state-of-the-art exposure to the concepts and technology of modern neuroscience. OHSU also offers certificate and degree programs, e.g. technology transfer and translational science, for advanced students in the NGP who want to broaden their career options.

Proper citation: Oregon Health and Science University Neuroscience Graduate Program (RRID:SCR_003508) Copy   

•   Source: SciCrunch Registry

https://www.vosesoftware.com/products/modelrisk/

Monte Carlo simulation software that makes quantitative risk analysis intuitive. Monte Carlo simulation Excel add-in that allows user to include uncertainty in their spreadsheet models.

Proper citation: ModelRisk (RRID:SCR_022836) Copy   

•   Source: SciCrunch Registry

https://www.palisade.com/risk/

Software is add-in tool for Microsoft Excel that computes and tracks many different possible scenarios in model using Monte Carlo simulation.Helps make better decisions through risk modeling and analysis.

Proper citation: atRISK (RRID:SCR_022837) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CHEMBIO

Ontology for Systems Chemical Biology and Chemogenomics

Proper citation: Systems Chemical Biology and Chemogenomics Ontology (RRID:SCR_003928) Copy   

•   Source: SciCrunch Registry

http://www.evidenceontology.org

A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2

Proper citation: ECO (RRID:SCR_002477) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/TGMA

A structured controlled vocabulary of the anatomy of mosquitoes.

Proper citation: Mosquito Gross Anatomy Ontology (RRID:SCR_003839) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/CPTAC

A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project

Proper citation: CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/ADW

An ontology for animal life history and natural history characteristics suitable for populations and higher taxonomic entities.

Proper citation: Animal Natural History and Life History Ontology (RRID:SCR_010292) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/COSTART

Ontology for coding, filing, and retrieving post-marketing adverse drug and biologic experience reports. It is organized in body system and pathophysiology hierarchies, as well as a separate fetal/neonatal category of less than 20 terms. COSTART has been superseded by the Medical Dictionary for Regulatory Activities (MedDRA) Terminology. For more information about MedDRA in the Metathesaurus, see the MedDRA source synopsis. COSTART was last updated in the Metathesaurus in 1999.

Proper citation: Coding Symbols for a Thesaurus of Adverse Reaction Terms (RRID:SCR_010294) Copy   

•   Source: SciCrunch Registry

http://purl.bioontology.org/ontology/HC

An ontology for courtship behavior of the spider Habronattus californicus. A demonstration of ontology construction as a general technique for coding ethograms and other descriptions of behavior into machine understandable forms.

Proper citation: Habronattus Courtship Ontology (RRID:SCR_010334) Copy   

•   Source: SciCrunch Registry