Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE, documented July 23, 2015. Of note: most functions have been integrated in 1000 Functional Connectomes Project (www.nitrc.org/projects/fcon_1000). This package is not updated, thus please visit 1000 Functional Connectomes Project site and download relevant bash scripts. BASH Scripts for a resting-state functional MRI study. The functions include seed-based correlation analysis, amplitude analysis and independent component analysis. Note: this tool is just a plug-in for FSL, AFNI and FreeSurfer. Thus, you need have them before you use BASH4RfMRI.

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• SciCrunch
• 15 years ago - by Anonymous

A database which provides a comprehensive and regularly updated collection of genetic association studies performed on multiple sclerosis phenotypes. Eligible publications are identified following systematic searches of scientific literature databases as well as the table of contents of journals in genetics, neurology, and immunology.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Provides technology platform to perform protein production and automated processes in context of biomolecular and biochemical screening assays.Through staff assisted screening, users have access to equipment including liquid handlers, plate readers and small molecule libraries.Unit is aimed at supporting the researchers of the CRG institute by purchasing, seeking and maintaining valuable stocks of clones and strains.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Dissemination of public datasets containing raw crystallography data (known as ''diffraction images''), along with rich metadata for search and persistent handles for citation in publications. Storage is federated, meaning the public index contains no data itself and merely points to data stored in external labs and institutions. TARDIS is scheduled to be replaced by the Bioscience Data Platform (https://www.nectar.org.au/bioscience-data-platform-tardis-cloud)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• SciCrunch
• 14 years ago - by Anonymous

A portal which provides simulation programs for nanoscale phenomena, online presentations, courses, learning modules, podcasts, animations, and teaching materials. Researchers can also collaborate with others and publish content.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.

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• SciCrunch
• 13 years ago - by Anonymous

Issues guidelines for nomenclature and classification of human biological targets, including targets of current and future prescription medicines. Works to facilitate interface between discovery of new sequences from Human Genome Project and designation of derived entities as functional biological targets and potential drug targets. Developes database which provides access to data on all known biological targets.

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• SciCrunch
• 16 years ago - by Anonymous

A portal which provides access to article level metrics, PLOS news, and videos and presentations. PLOS ALMs provides altmetrics for every article published in PLOS. Researchers can stay up-to-date with their published work and share information about the impact of their publications with collaborators, funders, institutions, and the research community at large.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript.

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• RRID-Legacy
• 7 years ago - by Anonymous

Over recent years, the European Commission has supported an increasing number of functional genomics projects focusing on the use of the laboratory mouse as a model of human disease. (see http://www.prime-eu.org/euromouseiiprojects.htm for a fuller listing of current and recent projects). CASIMIR (Coordination and Sustainability of International Mouse Informatics Resources: http://www.casimir.org.uk) is aimed at recommending standards to allow data sharing and integration between the different projects. CASIMIR spans a number of areas: data representation (in particular the use of shared ontologies), non-semantic, technical issues concerning database compatibility and interoperability, data acquisition, curation and ownership, integration of biological collections and material resources into the data network, and user interactions. As part of the CASIMIR initiative i-mouse.org was created as a common portal to CASIMIR and other resources we hope will be helpful for investigators using the mouse as a model system for humans or systems biologists and geneticists using the mouse as an experimental system. ontology; metadata;

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• SciCrunch
• 17 years ago - by Anonymous

A software tool (with GUI) for investigating inter-regional functional connectivity in event-related fMRI data and allows the user to assess the modulation of functional connectivity by an experimental condition.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software application to visualize the alignment of two genomic sequences together with their annotations. Used to generate print-quality images for comparative genome sequence analysis.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 19,2019.Database of tertiary structural modeling results of threading assembly refinement (TASSER) method for all 907 G protein-coupled receptors (GPCRs) in human genome. All sequences were collected from GPCR database http://www.gpcr.org/7tm/ and http://www.expasy.org/cgi-bin/lists?7tmrlist.txt. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. G protein-coupled receptors (GPCRs), encoded by about 5% of human genes, comprise the largest family of integral membrane proteins and act as cell surface receptors responsible for the transduction of endogenous signal into a cellular response. Although tertiary structural information is crucial for function annotation and drug design, there are few experimentally determined GPCR structures. To address this issue, we employ the recently developed threading assembly refinement (TASSER) method to generate structure predictions for all 907 putative GPCRs in the human genome. Unlike traditional homology modeling approaches, TASSER modeling does not require solved homologous template structures; moreover, it often refines the structures closer to native. These features are essential for the comprehensive modeling of all human GPCRs when close homologous templates are absent. Based on a benchmarked confidence score, approximately 820 predicted models should have the correct folds. The majority of GPCR models share the characteristic seven-transmembrane helix topology, but 45 ORFs are predicted to have different structures. This is due to GPCR fragments that are predominantly from extracellular or intracellular domains as well as database annotation errors. Our preliminary validation includes the automated modeling of bovine rhodopsin, the only solved GPCR in the Protein Data Bank. With homologous templates excluded, the final model built by TASSER has a global C(alpha) root-mean-squared deviation from native of 4.6 angstroms, with a root-mean-squared deviation in the transmembrane helix region of 2.1 angstroms. Models of several representative GPCRs are compared with mutagenesis and affinity labeling data, and consistent agreement is demonstrated. Structure clustering of the predicted models shows that GPCRs with similar structures tend to belong to a similar functional class even when their sequences are diverse. These results demonstrate the usefulness and robustness of the in silico models for GPCR functional analysis. Sponsors: GPCR is funded by the University at Buffalo, Buffalo, New York.

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• SciCrunch
• 17 years ago - by Anonymous

A Matlab package which contains six denoising filters and a noise estimation method for 4D DWI. The package includes nonlocal means, local PCA and Oracle DCT methods. Based on image redundancy and/or sparsity, the proposed filters provide efficient denoising while preserving fine structures.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Offers to run high-throughput compound, RNAi, and deletion library based screens for purpose of network analysis, drug and/or target discovery. Offers assistance to develop assay, carryout screen and/or analyze data. Equipment is also available for general (low-throughput) use. Helps with developing custom pipeline. Biomek FX liquid handling workstation with integrated Liconic shaker incubator (temperature, humidity, and CO2 controlled) can be used to setup and grow most cell types in 96 well plates. This robot is equipped to add RNAi constructs, drugs or other stimuli to each plate. Biomek FX can also be used to perform high-throughput biochemical assays. Cell based assays can be carried out using either Operetta CLS high-content analysis system or CLARIOstar plus. Both instruments have powerful, but easy to use software for data analysis.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software application that serves as a visualization tool to validate constructed genetic maps. CheckMatrix generates graphical genotypes and two-dimensional heat plots of pairwise scores. Visualization of regions with positive and negative linkage as well as of allele fraction per marker simplifies genetic map validation without applying statistical approaches. CheckMatrix works in conjunction with MadMapper and freely available at http://www.atgc.org/XLinkage/MadMapper/ (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

A software package which performs high-dimensional warping of brain images. Standard voxel-based analysis can be applied to these tissue density maps, in order to examine regional volumetrics, effects of disease, or correlations with clinical measurements.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

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• SciCrunch
• 7 years ago - submitted by Shuang Jiang

Ontology to help integrate species concepts with species occurrences, gene sequences, images, references and geographical information. See also Taxonconcept.org

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• SciCrunch
• 13 years ago - by Anonymous

A lightweight framework for setting up dependency-driven processing pipelines. The tool is essentially a configurable shell script (sh/bash), which can be included in other scripts and primarily provides a small number of utility functions for dependency checking and NFS-safe file locking for cluster processing.

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• SciCrunch
• 11 years ago - submitted by Kristen Jensen