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Software OLC-based de novo assembler for noisy long reads.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software for stepwise normalization functions for cDNA microarray data.

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• SciCrunch
• 13 years ago - by Anonymous

A center that conducts basic science and clinical research concerning spinal cord injury located at both the University of California San Francisco and the Zuckerberg San Francisco General Hospital.

• odc-sci
• 11 years ago - submitted by Adam Ferguson

Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A resource for sharing and collaboratively developing computational models of neural systems. While models can be submitted and developed in any format, the use of open standards such as NeuroML and PyNN is encouraged, to ensure transparency, modularity, accessibility and cross simulator portability. OSB will provide advanced facilities to analyze, visualize and transform models in these formats, and to connect researchers interested in models of specific neurons, brain regions and disease states. Research themes include: Basal ganglia modelling, Cerebellar Granule cell modelling, Cerebellar modelling, Hippocampal modelling, Neocortical modelling, Whole brain models. Additional themes are welcome.

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• SciCrunch
• 14 years ago - by Anonymous

A core facility which provides fee-based sample imaging and analysis using analytical and microscopy equipment to technology incubator clients, university researchers, and industry.

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• SciCrunch
• 14 years ago - by Anonymous

Software as neural network based method that focuses on identification of unstructured loops. Trained to distinguish between very long contiguous segments with non-regular secondary structure and well-folded proteins. Trained on predicted information rather than on experimental data.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

This resource provides a list of federal program officials in the neurosciences. An informal compendium of names and contact information for nearly 300 research grant and scientific review administrators in 21 organizational units.

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• SciCrunch
• 17 years ago - by Anonymous

Software tool for automatically scheduling events for rapid-presentation event-related (RPER) fMRI experiments (the schedule is the order and timing of events). Events in RPER are presented closely enough in time that their hemodynamic responses will overlap. This requires that the onset times of the events be jittered in order to remove the overlap from the estimate of the hemodynamic response. RPER is highly resistant to habituation, expectation, and set because the subject does not know when the next stimulus will appear or which stimulus type it will be.

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• SciCrunch
• 11 years ago - submitted by Maryann Martone

Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Data set of 48 healthy controls from a community (student) sample from Beijing Normal University in China with 3 resting state fMRI scans each. During the first scan participants were instructed to rest with their eyes closed. The second and third resting state scan were randomized between resting with eyes open versus eyes closed. In addition this dataset contains a 64-direction DTI scan for every participant. The following data are released for every participant: * 6-minute resting state fMRI scan (R-fMRI) * MPRAGE anatomical scan, defaced to protect patient confidentiality * 64-direction diffusion tensor imaging scan (2mm isotropic) * Demographic information and information on the counterbalancing of eyes open versus eyes closed.

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• SciCrunch
• 13 years ago - by Anonymous

Reconfigurable eukaryotic gene finder based on the Generalized Hidden Markov Model framework. The run time and memory requirements are linear in the sequence length. Genezilla utilizes Interpolated Markov Models (IMMs), Maximal Dependence Decomposition (MDD), and includes states for signal peptides, branch points, TATA boxes, and CAP sites.

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• RRID-Legacy
• 10 years ago - by Anonymous

Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Multi-center, randomized controlled study designed to determine if continuing interferon long term over several years will suppress the Hepatitis C virus, prevent progression to cirrhosis, prevent liver cancer and reduce the need for liver transplantation. Patient enrollment began in 2000 and was completed in 2003 at 10 clinical centers, which were supported by a data coordinating center, virological testing center, and central sample repository. Patients with chronic hepatitis C and advanced fibrosis or cirrhosis on liver biopsy who failed to respond to a previous course of interferon alfa were enrolled in this study. Patients were initially treated with a 24-week course of peginterferon alfa-2a and ribavirin. Patients who remained hepatitis C virus RNA positive were then randomized to receive maintenance, low-dose peginterferon or to be followed on no treatment. Liver biopsies were done before enrollment and after 2 and 4 years of treatment or follow-up. The endpoints were development of cirrhosis, hepatic decompensation, hepatocellular carcinoma, death, or liver transplantation. 1050 patients were randomized and followed through the 4 year randomized phase of the trial and as long as 4 years off treatment. Serum samples collected at multiple time points, DNA and liver tissue are available for scientific investigation.

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• dkNET
• 14 years ago - by Anonymous

Software application (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 1st, 2023. Coordinate based reference space for the mapping and registration of neuroanatomical data. Users can download image volumes representing the canonical Waxholm Space (WHS) adult C57BL/6J mouse brain, which include T1-, T2*-, and T2-Weighted MR volumes (generated at the Duke Center for In-Vivo Microscopy), Nissl-stained optical histology (acquired at Drexel University), and a volume of labels. All volumes are represented at 21.5μ isotropic resolution. Datasets are provided as gzipped NIFTI files.

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• SciCrunch
• 14 years ago - by Anonymous

A forward-based population genetics simulation program capable of simulating very complex evolution processes on large (think of millions) populations. Major features include variable population size; many built-in and hybrid (write in python) mutation, migration, selection models. simuPOP can be extended in Python so there is no limit on what you can do with it. (entry from Genetic Analysis Software)

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• SciCrunch
• 14 years ago - by Anonymous

Software suite of Docker images with customized R environments for particular tasks. Docker containers for R to create, distribute, deploy, and run software applications using containers.

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• RRID
• 3 years ago - by Anonymous

Collection of isogenic human cell lines that are deficient for the expression of single genes. The current collection is based on the human cell line KBM-7 (Kotecki et al. Experimental Cell Research 1999), which is haploid for all chromosomes except chromosome 8 and a small part of chromosome 15. In these cells, genes are disrupted by the means of a retroviral gene trap. The collection is being expanded to cover the majority of expressed genes. The Human Gene Trap Mutant Collection is generated as a public-private partnership between CeMM (the Research Center for Molecular Medicine of the Austrian Academy of Sciences) and Haplogen.

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• SciCrunch
• 14 years ago - by Anonymous