Curator Dashboard

Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

The NIDDK Information Network (dkNET) is a community-based network to serve needs of basic and clinical investigators that includes large pools of data and research resources relevant to mission of National Institute of Diabetes and Digestive and Kidney Disease.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

An R package that uses an individual-based approach to simulate distributions of genotypes that result from arbitrary within and among population demographies (including extinction/recolonization). These distributions can be used to test new or existing population-genetics summary statistics or develop null distributions under various demographies. (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous

Software R package for using R enviroments for annotation.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

An integrated and flexible software package for processing of DTI data, and in general for the correction of diffusion weighted images to be used for DTI and potentially for high angular resolution diffusion imaging (HARDI) analysis. It can be run on both Linux and Mac platforms. It is composed of two modules named DIFF PREP and DIFF CALC. * DIFF_PREP - software for image resampling, motion, eddy current distortion and susceptibility induced EPI distortion corrections, and for re-orientation of data to a common space * DIFF_CALC - software for tensor fitting, error analysis, color map visualization and ROI analysis In addition, TORTOISE contains additional Utilities, such as a tool for the analysis of multi-center phantom data.

• Resource
• SciCrunch
• 14 years ago - by Anonymous

An extensible framework for data-driven model parameter optimization that wraps and standardizes several existing open-source tools. BluePyOpt abstracts the optimization and evaluation tasks into various reusable and flexible discrete elements according to established best-practices. It also provides methods for setting up both small- and large-scale optimizations on a variety of platforms.

• Resource
• NIF
• 10 years ago - submitted by Matt Travers

Software R package for analysis of GRO-seq data. Used for identifying unannotated and cell type-specific transcription units from global run-on sequencing data

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Community standard for pathway data sharing. Standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Supports data exchange between pathway data groups and thus reduces complexity of interchange between data formats by providing accepted standard format for pathway data. Open and collaborative effort by community of researchers, software developers, and institutions. BioPAX is defined in OWL DL and is represented in RDF/XML format.Uses W3C standard Web Ontology Language, OWL.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Welcome to Michael Eisens lab in the Howard Hughes Medical Institute (HHMI) at University of California at Berkeley (UCB) and the Lawrence Berkeley National Lab (LBNL). We are part of the Department of Molecular and Cell Biology of UCB and the Genomics Division of LBNL, and the. We are located in Stanley Hall on the Berkeley campus.Our lab applies computational and experimental genomic approaches to study how genome sequences specify organismal form and function. We are particularly interested in the regulation of gene expression, and focus on how the information that specifies when and where genes are expressed is encoded in genome sequences, the role that regulated gene expression plays in animal development and the response of microbes to their environments, and how variation in and evolution of gene expression contributes to phenotypic variation and the remarkable diversity of life on Earth. This site contains a more detailed description of our research projects, an introduction to members of the lab, reprints of all of our publications, free downloadable and web-based software. Sponsor. Experimental work described here was supported by a Howard Hughes Medical Institute Investigator award to MBE and by National Institutes of Health (NIH) grant GM704403 to MBE and MDB. Computational analyses were supported in by NIH grant HG002779 to MBE. Work at Lawrence Berkeley National Laboratory was conducted under Department of Energy contract DE-AC02-05CH11231. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Software R package as molecular informatics toolkit with integration of bioinformatics and chemoinformatics tools for drug discovery.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Software package that implements generalized linear mixed model analysis of qRT-PCR data based on lognormal-Poisson model fitted using MCMC. Control genes are not required but can be incorporated as Bayesian priors or, when template abundances correlate with conditions, as trackers of global effects (common to all genes). Also implemented are the lognormal model for higher-abundance data and a classic model involving multi-gene normalization on a by-sample basis. Several plotting functions are included to extract and visualize results.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package for geodesic distance between phylogenetic trees and associated functions.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A software package for the simulation of deletions, insertions, inversions, tandem duplications and translocations of various sizes in any genome available as FASTA-file or data package in R. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.

• Resource
• SciCrunch
• 12 years ago - by Anonymous

Facility that provides access to high-speed cell sorting, analytical flow cytometry, imaging flow cytometry, and validated immune profiling spectral antibody panels. Core staff provide technical expertise in experiment design, data analysis, hardware and software training, operate the facility cell sorters, and are available to assist with analysis experiments for those who prefer to have their samples run by an expert cytometrist.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package for parallel estimation of mutual information based on entropy estimates from k-nearest neighbors distances and algorithms for reconstruction of gene regulatory networks.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any "thing", whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Core facility that aims to develop cell based disease models for screening and testing small molecules and drugs, and specializes in culture, scaling, and directed differentiation of human embryonic and induced pluripotent stem cells. It provides resources and expertise to researchers at the Institute and to their external partners to facilitate development of stem cell based assays and patient-specific disease models in screenable formats.

• Resource
• SciCrunch
• 10 years ago - submitted by Kristen Jensen

Software R package provides computational framework for analyzing mutations in immunoglobulin sequences. Immunoglobulin Somatic Hypermutation Analysis.

• Resource
• SciCrunch
• 3 years ago - submitted by Edyta Vieth

A software package to analyze next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. This software library makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. (entry from Genetic Analysis Software)

• Resource
• SciCrunch
• 14 years ago - by Anonymous