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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.
Proper citation: ARB project (RRID:SCR_000515) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 12,2023. Set of databases and tools that handle genomic and metagenomic sequences in their environmental contexts.Includes geographic information system to systematically store and analyse marine genomic and metagenomic data in conjunction with contextual information; environmental genome browser with fast search functionalities; database with precomputed analyses for selected complete genomes; database and tool to classify metagenomic fragments based on oligonucleotide signatures.
Proper citation: MeGX (RRID:SCR_000738) Copy
http://franklin.imgen.bcm.tmc.edu/
The mission of the Baylor College of Medicine - Shaw Laboratory is to apply methods of statistics and bioinformatics to the analysis of large scale genomic data. Our vision is data integration to reveal the underlying connections between genes and processes in order to cure disease and improve healthcare.
Proper citation: Baylor College of Medicine - Shaw Laboratory (RRID:SCR_000604) Copy
http://harvard.eagle-i.net/i/0000012e-58c7-d44f-55da-381e80000000
Core to provide gene expression data analysis service. Activities range from the provision of services to fully collaborative grant funded investigations.
Proper citation: Harvard Partners HealthCare Center for Personalized Genetic Medicine Bioinformatics Core Facility (RRID:SCR_000882) Copy
A lab organization which has bases in Munich, Germany and at Columbia University and focuses its research on protein structure and function using sequence and evolutionary information. They utilize machine learning and statistical methods to analyze genetic material and its gene products. Research goals of the lab involve using protein and DNA sequences along with evolutionary information to predict aspects of the proteins relevant to the advance of biomedical research.
Proper citation: ROSTLAB (RRID:SCR_000792) Copy
http://www.scienceexchange.com/facilities/macquarie-university
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 23,2023. Set of facilities based out of Macquarie University in New South Wales. Some facilities provide services such as proteome analysis or resources of various academic departments like engineering, biological sciences, and geography.
Proper citation: Macquarie University Labs and Facilities (RRID:SCR_000944) Copy
A genome browser specialized in next-generation sequencing data.
Proper citation: GenomeJack (RRID:SCR_012026) Copy
Specializes in sequence and array-based SNP and copy number analysis, genetic association software, and analytic services. Their technologies empower scientists to determine the genetic causes of disease, transform drug discovery, develop genetic diagnostics, and advance the quest for personalized medicine.
Proper citation: Golden Helix Incorporated (RRID:SCR_012191) Copy
Functional genomic database for malaria parasites. Database for Plasmodium spp. Provides resource for data analysis and visualization in gene-by-gene or genome-wide scale. PlasmoDB 5.5 contains annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution data. Data can be queried by selecting from query grid or drop down menus. Results can be combined with each other on query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.Key community database for malaria researchers, intersecting many types of laboratory and computational data, aggregated by gene.
Proper citation: PlasmoDB (RRID:SCR_013331) Copy
https://www.leica-microsystems.com/products/microscope-software/details/product/leica-las-x-ls/
Software for image capture, processing and analysis with Leica fluorescence and confocal microscopes.
Proper citation: Leica Application Suite X (RRID:SCR_013673) Copy
http://www.cyto.purdue.edu/flowcyt/software/Winmdi.htm
Software to analyze flow cytometry listmode data files.
Proper citation: WinMDI Software (RRID:SCR_013745) Copy
A universal tracking application specifically designed to support animal behavioral analysis. AnimalTracker consists of three main modules which can be used independently: Tracker is responsible for image processing and providing the coordinates of the identified object; Zone Designer provides tools to create custom-made investigation areas in order to design a maze-setup; and Tracking Analyzer module serves to define and obtain the parameters needed for the evaluation.
Proper citation: AnimalTracker (RRID:SCR_014397) Copy
http://bioconductor.org/packages/edgeR/
Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.
Proper citation: edgeR (RRID:SCR_012802) Copy
http://www.bioconductor.org/packages/release/bioc/html/affy.html
Software R package of functions and classes for the analysis of oligonucleotide arrays manufactured by Affymetrix. Used to process probe level data and for exploratory oligonucleotide array analysis.
Proper citation: affy (RRID:SCR_012835) Copy
Ratings or validation data are available for this resource
http://ccb.jhu.edu/software/tophat/index.shtml
Software tool for fast and high throughput alignment of shotgun cDNA sequencing reads generated by transcriptomics technologies. Fast splice junction mapper for RNA-Seq reads. Aligns RNA-Seq reads to mammalian-sized genomes using ultra high-throughput short read aligner Bowtie, and then analyzes mapping results to identify splice junctions between exons.TopHat2 is accurate alignment of transcriptomes in presence of insertions, deletions and gene fusions.
Proper citation: TopHat (RRID:SCR_013035) Copy
Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration.
Proper citation: Neuroimaging in Python (RRID:SCR_013141) Copy
http://www.leaddiscovery.co.uk/
LeadDiscovery was founded by life scientists to expedite drug discovery and pharmaceutical development. Based on a solid background of experience from within the pharmaceutical research and development sector, the aim of this resource is to help companies optimize drug discovery and product pipelines through the identification of breaking research and the in depth and expert evaluation of selected therapeutic areas. At the same time it also provides a showcase for pharmaceutical, biotechnology and academic organizations wishing to increase the exposure of their research to the drug development community. LeadDiscovery sits at the center of this sector helping companies to identify commercially viable R&D options from within small biotechs and the public sector. Additionally, it supports the drug discovery and pharmaceutical development community through three key services: DailyUpdates, UpdatesPlus and PharmaReports - DailyUpdates: Launched in 2002 this popular e-mail alert service delivers information on breaking research, new clinical trials, drug development news and recently published market research and pipeline analysis reports. Registration to receive the service is available here - UpdatesPlus: Developed in 2007 as an extension of DailyUpdates, UpdatesPlus provides a monthly in depth analysis of breaking research and development activity in high profile therapeutic areas. - PharmaReports: LeadDiscovery offers a wide range of in depth pharmaceutical reports. It''s reports include market research reports and pipeline analyses. You can search our entire portfolio using LeadDiscovery''s search engine. Alternatively as it are one of the few information providers that has extensive research and development experience, LeadDiscovery occupys a unique position of being able to source reports that accurately meet your needs. If we don''t have a report that fits your requirements, it can produce one through its pharmaceutical consultancy services. LeadDiscovery offers full reports in selected areas of the pharmaceutical and biotech sector. Each of the reports below has been especially selected by LeadDiscovery and categorized into relevant areas: - Oncology - Cancer Immunotherapy - Immunology & Inflammatory Diseases - Infectious Diseases - Psychiatric, Addictive & Sleep Disorders - Pain - Neurodegenerative & Neuroelectrophysiological Disorders - Metabolic & Hormonal Disorders - Cardiovascular Disorders - GenitoUrinary Tract Disorders - Technology - Diagnostics & Devices - Other Theraputic Areas, Pharmaceutical Strategy and Development
Proper citation: LeadDiscovery: Providing Information to the Drug Discovery Sector (RRID:SCR_006464) Copy
A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.
Proper citation: Jalview (RRID:SCR_006459) Copy
http://bioconductor.org/packages/bioc/html/GeneAnswers.html
GeneAnswers provide an integrated tool for given genes biological or medical interpretation. It includes statistical test of given genes and specified categories. Microarray techniques have been widely employed in genomic scale studies for more than one decade. The standard analysis of microarray data is to filter out a group of genes from thousands of probes by certain statistical criteria. These genes are usually called significantly differentially expressed genes. Recently, next generation sequencing (NGS) is gradually adopted to explore gene transcription, methylation, etc. Also a gene list can be obtained by NGS preliminary data analysis. However, this type of information is not enough to understand the potential linkage between identified genes and interested functions. The integrated functional and pathway analysis with gene expression data would be very helpful for researchers to interpret the relationship between the identified genes and proposed biological or medical functions and pathways. The GeneAnswers package provides an integrated solution for a group of genes and specified categories (biological or medical functions, such as Gene Ontology, Disease Ontology, KEGG, etc) to reveal the potential relationship between them by means of statistical methods, and make user-friendly network visualization to interpret the results. Besides the package has a function to combine gene expression profile and category analysis together by outputting concept-gene cross tables, keywords query on NCBI Entrez Gene and application of human based Disease ontology analysis of given genes from other species can help people to understand or discover potential connection between genes and functions. Sponsors: This project was supported in part by Award Number UL1RR025741 from the National Center for Research Resources.
Proper citation: GeneAnswers (RRID:SCR_006498) Copy
http://www.geenivaramu.ee/en/tools/gwama
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for meta analysis of whole genome association data.
Proper citation: GWAMA (RRID:SCR_006624) Copy
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