Curator Dashboard

Software application for diverse collection of scripts that perform useful and common FASTA/FASTQ manipulation tasks, such as filtering, merging, splitting, sorting, trimming, search/replace, etc. Input and output files can be gzipped (format is automatically detected) and individual Fastaq commands can be piped together.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

The CellML language is an open standard based on the XML markup language. The purpose of CellML is to store and exchange computer-based mathematical models. CellML allows scientists to share models even if they are using different model-building software. It also enables them to reuse components from one model in another, thus accelerating model building. Although CellML was originally intended for the description of biological models; CellML includes information about model structure (how the parts of a model are organizationally related to one another), mathematics (equations describing the underlying processes) and metadata (additional information about the model that allows scientists to search for specific models or model components in a database or other repository). The CellML team is committed to providing freely available tools for creating, editing, and using CellML models. We provide information regarding tools we are developing internally and links to external projects developing tools which utilize the CellML format. Please let us know if you have an open source CellML tool looking for a home on the internet, as we are able to offer limited hosting services on cellml.org.

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• SciCrunch
• 15 years ago - by Anonymous

A database that contains brain imaging data collected on 3T MRI scanners from over 200 normally developing healthy children from birth to 18 years. The imaging data stored in the C-MIND database are DTI, HARDI, 3DT1W, 3DT2W, concurrent ASL-BOLD scans during two language tasks (Stories and Sentence-Picture Matching), Resting State fMRI and Baseline ASL scans.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.

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• RRID-Legacy
• 6 years ago - submitted by Fan Jiang

A list of information about key sources of funding in various countries worldwide, from the SfN. The listings below include notes about each funding agency''s area of research and type of funding, as well as information about special funding opportunities. Most funders have multifaceted programs and schemes, and more detailed information can be found by following the links provided. You can download a PDF version of the entire directory or browse the links below that will take you directly to the funders'' Web sites. SfN welcomes suggestions or changes to existing information; please contact globalaffairs @ sfn.org.

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• SciCrunch
• 16 years ago - by Anonymous

A software package which contains tools for doing group analysis of FreeSurfer surface data using the general linear model in R (lm). Results can be rendered in FreeSurfer freeview or AFNI SUMA. Plots for selected vertices can be rendered in R with ggplot2.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool for precision HLA typing from next generation sequencing data.

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• dkNET
• 4 years ago - submitted by Ko-Wei Lin

While the traditional temporally concatenated Group ICA (TC-GICA) adopting three steps of PCA reduction, it could result in inconsistent and variable components when different subject orders were used, both for the group- and individual-level results. Such instability can further cause instable and thus unreliable statistical results. Subject Order-Independent Group ICA (SOI-GICA) aims to fix this problem by producing stable and reliable GICA results. For details please see the paper Subject Order-Independent Group ICA (SOI-GICA) for Functional MRI Data Analysis (Zhang et al., 2010, NeuroImage)(http://dx.doi.org/10.1016/j.neuroimage.2010.03.039). MICA is the toolbox inplemented SOI-GICA for convenience of usage.

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• SciCrunch
• 14 years ago - by Anonymous

A tractography algorithm for HARDI which provides a relatively accurate and efficient fiber tracking mechanism by reconstructing a bi-tensor model for underlying signals and exploiting intrinsic operations on the space of diffusion tensors. Given HARDI data sets, IUKF is capable of tracking in the presence of complex local geometries, such as crossing and kissing fibers. Reconstruction is only performed at the voxels along estimated fibers.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool to assemble bacterial isolate genomes from Illumina paired end reads. Used for isolate data only, primarily small haploid organisms. Supports assemblers like SKESA, Velvet and Megahit.

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• RRID-Legacy
• 8 years ago - submitted by Dan Fornika

researchobject.org is a community web page that presents the ongoing activities of the open Research Object community and gathers knowledge about related developments and adoptions. The community is composed of representatives from science domains, research infrastructure development, publishing and policy making. The vision of the community is to facilitate knowledge interchange and reproducible computational research through the definition and promotion of Research Object principles, i.e. identification, annotation, and aggregation of scientific artefacts. The focus is not on replacing any solutions that are already in place, but on ''engaging'' with existing solutions.

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• SciCrunch
• 13 years ago - by Anonymous

A statistical analysis tool for manifold-valued data. The SPD manifold for diffusion tensor images (DTI) and the Hilbert unit sphere for square root representation of orientation distribution functions (ODF) can be used.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

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• RRID-Legacy
• 9 years ago - by Anonymous

PhenomicDB is a multi-organism phenotype-genotype database including human, mouse, fruit fly, C.elegans, and other model organisms. The inclusion of gene indices (NCBI Gene) and orthologs (same gene in different organisms) from HomoloGene allows to compare phenotypes of a given gene over many organisms simultaneously. PhenomicDB contains data from publicly available primary databases: FlyBase, Flyrnai.org, WormBase, Phenobank, CYGD, MatDB, OMIM, MGI, ZFIN, SGD, DictyBase, NCBI Gene, and HomoloGene. We brought this wealth of data into a single integrated resource by coarse-grained semantic mapping of the phenotypic data fields, by including common gene indexes (NCBI Gene), and by the use of associated orthology relationships (HomoloGene). PhenomicDB is thought as a first step towards comparative phenomics and will improve the understanding of the gene functions by combining the knowledge about phenotypes from several organisms. It is not intended to compete with the much more dedicated primary source databases but tries to compensate its partial loss of depth by linking back to the primary sources. The basic functional concept of PhenomicDB is an integrated meta-search-engine for phenotypes. Users should be aware that comparison of genotypes or even phenotypes between organisms as different as yeast and man can have serious scientific hurdles. Nevertheless finding that the phenotype of a given mouse gene is described as ��similar to psoriasis�� and at the same time that the human ortholog has been described as a gene causing skin defects can lead to novelty and interesting hypotheses. Similarly, a gene involved in cancer in mammalian organisms could show a proliferation phenotype in a lower organism such as yeast and thus, give further insights to a researcher.

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• SciCrunch
• 17 years ago - by Anonymous

Software for efficient generation and simulation of models containing stochastic ion channels distributed across dendritic and axonal membranes. It computes the behavior of neurons taking account of the stochastic nature of ion channel gating and the detailed positions of the channels themselves. It is designed as a complement for existing tools.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software package provides functionalities for downstream analysis, annotation and visualizaton of alternative splicing events. Mapping alternative splicing events to proteins.

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• RRID
• 3 years ago - by Anonymous

Portal that aims to inspire connections, clinical advances and accelerate progress toward multiple sclerosis cures. MSDF updates its site with news and information about topics relevant to multiple sclerosis and hosts discussions about controversial subjects with the goal of spreading information and enabling collaboration between researchers. MSDF provides access to drug development pipelines, tissue repositories, the MS gene, animal models, and clinical trials.

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• SciCrunch
• 13 years ago - by Anonymous

A software package for the real-time analysis and dynamic visualization of functional magnetic resonance imaging data sets. It allows users to observe the working brain "online" by incrementally computing statistical maps as contrasts of a General Linear Model (GLM). The program also performs real-time pre-processing, including 3D motion correction, spatial Gaussian smoothing and temporal filtering (drift removal).

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software R package for detection, characterization and visualization of localized hypermutated regions, often referred to as kataegis. Aims to identify putative kataegis loci from common data formats housing genomic variants.

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• RRID
• 3 years ago - submitted by Daan Hazelaar

THIS RESOURCE IS NO LONGER IN SERVICE.Documented on August 23,2022. An open source tool developed for genome-wide detection of fusion transcripts from human being paired-end RNA-Seq data. This tool is a part of a larger set of tools to efficiently align oligonucleotides onto reference sequences .

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• SciCrunch
• 13 years ago - by Anonymous