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https://www.molinspiration.com/

Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.

Proper citation: Molinspiration (RRID:SCR_018525) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=meta

Software general R package providing standard methods for meta analysis.

Proper citation: meta (RRID:SCR_019055) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/projects/gmac_2012/

Open-source software toolbox implemented multivariate spectral Granger Causality Analysis for studying brain connectivity using fMRI data. Available features are: fMRI data importing, network nodes definition, time series preprocessing, multivariate autoregressive modeling, spectral Granger causality indexes estimation, statistical significance assessment using surrogate data, network analysis and visualization of connectivity results. All functions are integrated into a graphical user interface developed in Matlab environment. Dependencies: Matlab, BIOSIG, SPM, MarsBar.

Proper citation: GMAC: A Matlab toolbox for spectral Granger causality analysis of fMRI data (RRID:SCR_009581) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/gppi/

An automated toolbox for a generalized form of psychophysiological interactions for SPM and FSFAST. The automated toolbox can do the following: (a1) produce identical results to the current implementation in SPM (a2) use the current implementation of PPI in SPM but using the regional mean instead of the eigenvariate (a3) use a generalized form that allows a PPI for each task to be in the same model using either the regional mean of eigenvariate (b) create the model using the output of one of the (a) options and the first level design (c) estimate the model (/results directory) (d) compute the contrasts specified.

Proper citation: Generalized PPI Toolbox (RRID:SCR_009489) Copy   

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http://scirus.com/

Science-specific search engine with over 575 million scientific items indexed at last count (May 2013), it allows researchers to search for not only journal content but also scientists'' homepages, courseware, pre-print server material, patents and institutional repository and website information. Scirus helps you quickly locate scientific information on the Web: * Filters out non-scientific sites. For example, if you search on REM, Google finds the rock group - Scirus finds information on sleep, among other things * Finds peer-reviewed articles such as PDF and PostScript files, which are often invisible to other search engines. * Searches the most comprehensive combination of web information, preprint servers, digital archives, repositories and patent and journal databases. Scirus goes deeper than the first two levels of a Web site, thereby revealing much more relevant information. Scirus has proved so successful at locating science-specific results on the Web that the Search Engine Watch Awards voted Scirus ''Best Specialty Search Engine'' in 2001 and 2002 and ''Best Directory or Search Engine Website'' WebAward from Web Marketing Association in 2004, 2005, 2006 and 2007. Give your Web site greater functionality and enhance the experience of your users, by adding Scirus to your home page for free. Scirus uses the latest in search engine technology to pinpoint precise scientific information that other search engines can not reach, including pdf files and peer reviewed articles. Make your Web site more visible to the scientific community, by submitting it for inclusion on Scirus. You will increase the chance of scientists finding your site when looking for information and you could increase your visitor rate.

Proper citation: Scirus - for scientific information only (RRID:SCR_010657) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/CpGassoc/index.html

Software R package to test association between methylation at CpG sites across genome and phenotype of interest, adjusting for any relevant covariates. Can perform standard analyses of large datasets without need to manually input data. Can handle mixed effects models with chip or batch entering model as random intercept. Includes tools to apply quality control filters, perform permutation tests, and create QQ plots, manhattan plots, and scatterplots for individual CpG sites.

Proper citation: CpGassoc (RRID:SCR_000320) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapE15_5_01.htm

Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint E15 Atlas (RRID:SCR_002786) Copy   

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http://cmbn-approd01.uio.no/zoomgen/hippocampus/home.do

An interactive reference atlas providing a systematic overview of cyto- and chemoarchectonical features of the hippocampus proper, fasciola, and associated parahippocampal cortices. This atlas system has been developed to serve the need to integrate detailed descriptions of structures and criteria defining boundaries and atlas images in which the underlying histological features can be explored. Features * Alphabetical and hierarchical overview of 18 hippocampal structures * Detailed, illustrated descriptions of 63 boundaries * Interactive image repository with ~100 coronal histological images stained for NeuN, calbindin, and parvalbumin * Triple image viewer in which differently stained neighboring sections can be interactively compared * Graphical overlay of substructures based on described boundary criteria * Bidirectional links between structure descriptions and image repository The atlas is based on histological material from an adult Long Evans rat, stained for NeuN, calbindin, and parvalbumin. The system is intended for researchers working in the field, as well as students interested in this brain region. The atlas is accessed through the structure index or image viewer. Re-use of data from this repository is allowed provided that reference is given to the publication.

Proper citation: Rat Hippocampus Atlas (RRID:SCR_005552) Copy   

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http://www.nitrc.org/projects/sri24/

An MRI-based atlas of normal adult human brain anatomy, generated by template-free nonrigid registration from images of 24 normal control subjects. The atlas comprises T1, T2, and PD weighted structural MRI, tissue probability maps (GM, WM, CSF), maximum-likelihood tissue segmentation, DTI-based measures (FA, MD, longitudinal and transversal diffusivity), and two labels maps of cortical regions and subcortical structures. The atlas is provided at 1mm isotropic image resolution in Analyze, NIFTI, and Nrrd format. We are also providing an experimental packaging for use with SPM8.

Proper citation: SRI24 Atlas: Normal Adult Brain Anatomy (RRID:SCR_002551) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapP7_01.htm

Abbreviated reference atlas for the P56 mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint P7 Atlas (RRID:SCR_002787) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/unc_brain_atlas

Human brain atlases for adult, pediatric and elderly populations, by iterative joint deformable registration of training datasets into a single unbiased average image. Atlases packages include T1-weighted images, tissue priors (WM,GM,CSF), lobar parcellation maps and subcortical structures. Current available atlases: * Adult atlas: Symmetric atlas generated from 50+ healthy adult subjects (20-59 year old). * UNC-MNI Pediatric 1-year-old atlas: Symmetric atlas generated from 104 1-year-old subjects, combining children at high familial risk of autism and controls. * Pediatric 4-year-old atlas: Symmetric atlas generated from 10 4-year-old healthy subjects. * Elderly atlas: Atlas generated from 27 healthy elderly subjects (60+ years old). Additional information and acknowledgment for their usage can be found by clicking on the release notes.

Proper citation: UNC Human Brain Atlas (RRID:SCR_002606) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/R0_1.htm

A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines.

Proper citation: GenePaint Interactive Anatomy Atlas (RRID:SCR_007680) Copy   

•   Source: SciCrunch Registry

http://www.genboree.org/epigenomeatlas/index.rhtml

Collection of human reference epigenomes and results of their integrative and comparative analyses. Successive releases of the Atlas will provide progressively more detailed insights into locus-specific epigenomic states, including histone marks and DNA methylation marks across specific tissues and cell types, developmental stages, physiological conditions, genotypes, and disease states. The Human Epigenome Atlas is produced by the NIH Epigenomics Roadmap Consortium.

Proper citation: Human Epigenome Atlas (RRID:SCR_006153) Copy   

•   Source: SciCrunch Registry

http://www.iit.edu/~mri/

Atlas that contains new anatomical, DTI, HARDI templates and probabilistic gray matter labels of the adult human brain in ICBM-152 space. Artifact-free MRI data from 72 human subjects was used in the development of the atlas. All diffusion MRI data collection was conducted using Turboprop, and spatial normalization was accomplished in a population-based fashion. A description of the contents of the atlas can be found in the Downloads link. NOTE: The files of the older IIT2 DTI Brain Template are still available. However, the new DTI template of the IIT Human Brain Atlas (v.3) is of superior quality and allows more accurate registration across subjects.

Proper citation: IIT Human Brain Atlas (RRID:SCR_009587) Copy   

•   Source: SciCrunch Registry

https://www.facebase.org/fishface/home

ishFace is an atlas of zebrafish craniofacial development. How do the elements of the craniofacial skeleton arise, grow, and reshape? Answers to this question are coming from both molecular-genetic and cell-biological approaches, which rely, first of all, on precise description of the developmental events and processes that comprise skeletogenesis. Zebrafish, with a sophisticated knowledge of its genetics and genomics, with favorable attributes for phenotypic analyses of development, and with patterns of development conserved among all vertebrates, provides a powerful animal model for learning about craniofacial development. In particular, with current transgenic approaches one can examine craniofacial skeletal elements in exquisite cellular detail during an extended period of development within living, intact embryos and larvae an investigative method unsurpassed in accuracy and sensitivity. We constructed this developmental atlas of the craniofacial skeleton, FishFace, to serve as a guide for such study. We hope that the FishFace Atlas will be particularly useful in comparative and mutational analyses where there is interest in understanding the cellular basis of early skeletogenesis. The heart of the FishFace Atlas uses high magnification (generally a 40x objective) confocal image stacks showing transgenically-labelled chondrocytes or osteoblasts, along with mineralized bone matrix, which is visualized by vital staining with Alizarin red. We present these stacks in sequences that follow particular individual cartilages and bones of the first two pharyngeal arches as they develop during embryonic and larval stages. To do so, we build on the foundation set out in the gold standard reference for describing comprehensively skeletal elements in the zebrafish craniofacial complex, Cubbage and Mabee (1996), which used fixed preparations stained for cartilage and bone through adult stages. The FishFace Atlas element development section adds considerable detail to arch one and two early development, particularly at the cellular level, but also in description of element growth and shaping. Other sections of the FishFace Atlas, at lower magnification, provide anatomical context for the element development section, including an interactive tool made by optical projection tomography (OPT) for learning the anatomy of the entire larval skull. Hence, the FishFace Atlas provides the community with an interactive resource with which the user can understand not only the cellular details, but also complex 3D anatomical relationships, of developing elements in the craniofacial skeleton of the zebrafish.

Proper citation: FishFace - An atlas of zebrafish craniofacial development (RRID:SCR_008894) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/inia19/

Primate brain atlas created from over 100 structural MR scans of 19 rhesus macaque animals. The atlas currently comprises high-resolution T1-weighted average MR images with and without skull stripping, tissue probability maps, and a detailed parcellation map based on the NeuroMaps atlas.

Proper citation: INIA19 Primate Brain Atlas (RRID:SCR_009498) Copy   

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http://www.nitrc.org/projects/r-spit/

Group ICA (Independent Component Analysis) was used to generate spatial templates for 12 common resting-state networks in 62 typically-developing children, ages 9-15. They have made these available for those that will find them useful for masking and spatial template matching procedures. Basic demographic data on the sample is provided along with the protocol used to generate the templates.

Proper citation: resting-state pediatric imaging template (RRID:SCR_009647) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/ICBM152NLin2009

Unbiased standard magnetic resonance imaging template brain volume for normal population. These volumes were created using data from ICBM project. 6 different templates are available: * ICBM 2009a Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, also T2 relaxometry (T2 values calculated for each subject using single dual echo PD/T2 scan), and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.10.1. * ICBM 2009a Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.10.1. Also included brain mask, eye mask and face mask. * ICBM 2009b Nonlinear Symmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009b Nonlinear Asymmetric - template which includes only T1w,T2w and PDw modalities. * ICBM 2009c Nonlinear Symmetric - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Also included lobe atlas used for ANIMAL+INSECT segmentation, brain mask, eye mask and face mask. Intensity inhomogeneity was performed using N3 version 1.11. Sampling is different from 2009a template. * ICBM 2009c Nonlinear Asymmetric template - template which includes T1w,T2w,PDw modalities, and tissue probabilities maps. Intensity inhomogeneity was performed using N3 version 1.11 Also included brain mask, eye mask and face mask.Sampling is different from 2009a template. All templates are describing the same anatomy, but sampling is different. Also, different versions of N3 algorithm produces slightly different tissue probability maps. Tools for using these atlases can be found in the Software section. Viewing the multiple atlas volumes online requires Java browser support. You may also download the templates - see licensing information.

Proper citation: ICBM 152 Nonlinear atlases version 2009 (RRID:SCR_008796) Copy   

•   Source: SciCrunch Registry

http://www.bic.mni.mcgill.ca/ServicesAtlases/NIHPD-obj1

An unbiased standard magnetic resonance imaging template brain volume for pediatric data from the 4.5 to 18.5y age range. These volumes were created using data from 324 children enrolled in the NIH-funded MRI study of normal brain development (Almli et al., 2007, Evans and Group 2006). Tools for using these atlases can be found in the Software section. To view the atlases online, click on the appropriate JIV2 link in the Download section. You can download templates constructed for different age ranges. For each age range you will get an average T1w, T2w, PDw maps normalized between 0 and 100 and tissue probability maps, with values between 0 and 1. Also each age range includes a binary brain mask.

Proper citation: NIHPD Objective 1 atlases (4.5 - 18.5y) (RRID:SCR_008794) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=GenBinomApps

Software R package as collection of functions to compute the Clopper-Pearson Confidence Interval and the required sample size. Density, distribution function, quantile function and random generation for the Generalized Binomial Distribution.Enhanced model for burn-in studies, where failures are tackled by countermeasures.

Proper citation: GenBiomApps (RRID:SCR_025542) Copy   

•   Source: SciCrunch Registry