Curator Dashboard

Vector Core produces gene transfer vectors that facilitate transfer of specific genes into either normal or aberrant cells. Provides intellectual and technical advice to researchers regarding the optimal use of these systems.

• Resource
• RRID
• 1 year ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 2nd, 2023. Sequence composition based classifier for metagenomic sequences. It works by capturing signatures of each sequence based on the sequence composition. Each sequence is modeled as a walk in a de Bruijn graph with underlying Markov chain properties. ClaMS captures stationary parameters of the underlying Markov chain as well as structural parameters of the underlying de Bruijn graph to form this signature. In practice, for each sequence to binned, such a signature is computed and matched to similar signatures computed for the training sets. The best match that also qualifies the normalized distance cut-off wins. In the case that the best match does not qualify this cut-off, the sequence remains un-binned.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Web server for anisotropy of diffraction limit and Bayesian estimation of structure amplitudes by Global Phasing Limited. Server uses DEBYE and STARANISO software to perform anisotropic cut off of merged intensity data, to perform Bayesian estimation of structure amplitudes and to apply anisotropic correction to data.

• Resource
• RRID-Legacy
• 7 years ago - by Anonymous

Simulation lab that is designed as home. Provides space to researchers who want to observe participant behavior in more realistic environment. Offers environment that feels authentic and natural to human condition.

• Resource
• RRID
• 1 year ago - submitted by Edyta Vieth

A database containing genome-wide brain DNA methylation profiles for human and mouse brains. The DNA methylation profiles were generated by Methylation Mapping Analysis by Paired-end Sequencing (Methyl-MAPS) method and analyzed by Methyl-Analyzer software package. The methylation profiles cover over 80% CpG dinucleotides in human and mouse brains in single-CpG resolution. The integrated genome browser (modified from UCSC Genome Browser allows users to browse DNA methylation profiles in specific genomic loci, to search specific methylation patterns, and to compare methylation patterns between individual samples. Two species were included in the Brain Methylome Database: human and mouse. Human postmortem brain samples were obtained from three distinct cortical regions, i.e., dorsal lateral prefrontal cortex (dlPFC), ventral prefrontal cortex (vPFC), and auditory cortex (AC). Human samples were selected from our postmortem brain collection with extensive neuropathological and psychopathological data, as well as brain toxicology reports. The Department of Psychiatry of Columbia University and the New York State Psychiatric Institute have assembled this brain collection, where a validated psychological autopsy method is used to generate Axis I and II DSM IV diagnoses and data are obtained on developmental history, history of psychiatric illness and treatment, and family history for each subject. The mouse sample (strain 129S6/SvEv) DNA was collected from the entire left cerebral hemisphere. The three human brain regions were selected because they have been implicated in the neuropathology of depression and schizophrenia. Within each cortical region, both disease and non-psychiatric samples have been profiled (matching subjects by age and sex in each group). Such careful matching of subjects allows one to perform a wide range of queries with the ability to characterize methylation features in non-psychiatric controls, as well as detect differentially methylated domains or features between disease and non-psychiatric samples. A total of 14 non-psychiatric, 9 schizophrenic, and 6 depression methylation profiles are included in the database.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Python interface to graph visualization software Graphviz Dot.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Core provides services for acquiring three-dimensional imaging and quantitative analysis of biological and engineered structures/materials. The core is capable of imaging mineralized tissues (e.g., bone, teeth) and soft tissues (e.g., tendons, ligaments, cartilage, blood vessels, muscle) with the aid of radiographic contrast agents. This core is managed and operated by members of the Orthopaedic Research Laboratories.

• Resource
• RRID
• 1 year ago - submitted by Edyta Vieth

A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

• Resource
• SciCrunch
• 13 years ago - by Anonymous

Software tool based on hashing algorithm and approach to genomic reference indices from Noblis. Used to indexing genomic references. Aligns reads on reference genomes at random positions where k-mer indexes are matched with reference genomes.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Nathan Anderson

Software R package for random forests regression, classification, survival analysis, competing risks, multivariate, unsupervised, quantile regression, and class imbalanced q-classification. Extreme random forests and randomized splitting. Suite of imputation methods for missing data.

• Resource
• RRID
• 1 year ago - by Anonymous

Biomedical Logical Programming (Blip) is a research-oriented deductive database and prolog application library for handling biological and biomedical data. It includes packages for advanced querying of ontologies and annotations. Blip underpins the Obol tool. Here are some distinguishing characteristics of Blip * Lightweight. Bloat-free: Blip only has as many modules as it needs to do its job. * Fast. * Declarative. Say what you want to do, not how you want to do it * Blip can be Query-oriented: specify your data sources and ask your query * Blip can be Application-oriented: it is designed to be used as an application library used by other bioinformatics tools * Mature and fully functional ontology module for handling both OBO-style ontologies and OWL ontologies. * Modules for handling biological sequences and sequence features. (currently limited functionality, added as needed) * A systems biology module for querying pathway and interaction data. (currently limited functionality, added as needed) * Relational database integration. SQL can be viewed as a highly restricted dialect of Prolog. Although the SWI-Prolog in-memory database is fast and scalable, sometimes it is nice to be able to fetch data from an external database. Blip contains a generic SQL utility module and predicate mappings for the GO database, Ensembl and Chado * Integration with a variety of bioinformatics file formats. SWI-Prolog has a variety of fast libraries for dealing with XML, RDF and tabular data files. Blip provides bridges from bio file formats encoded using these syntaxes into its native models. For other syntaxes, Blip seamlessly integrates other packages such as BioPerl and go-perl. Although these dependencies require extra installation, there is no point reinventing the wheel * Rapid development of web applications. Blip extends SWI-Prolog''''s excellent http support with a simple and powerful logical-functional-programming style application server, serval. This has been used to prototype a fully-featured next-generation replacement for the GO project amigo browser. * Scalable. Blip is not intended to be a toy system on toy data (although it is happy to be used as a toy if you like!). It is intended to be used as an application component and a tool operating on real-world biological and biomedical data Blip is written in SWI-Prolog, a fast, robust and scalable implementation of ISO Prolog. Platform: Windows compatible, Mac OS X compatible, Linux compatible, Unix compatible

• Resource
• SciCrunch
• 15 years ago - by Anonymous

Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

• Resource
• RRID-Legacy
• 7 years ago - submitted by Nathan Anderson

Provides facilities for (U-Th)/He thermochronology on variety of accessory minerals, including apatite, sphene, monazite and zircon. The low closure temperature of the (U-Th)/He system in these minerals makes it ideal for application to geological problems in geomorphology, surface processes, tectonics, structural geology, basin evolution, and thermal maturation.

• Resource
• RRID
• 1 year ago - submitted by Edyta Vieth

A database of human molecular interaction networks that integrates human protein-protein and transcriptional regulatory interactions from 15 distinct resources and aims to give direct and easy access to the integrated data set and to enable users to perform network-based investigations. The database includes tools (i) to search for molecular interaction partners of query genes or proteins in the integrated dataset, (ii) to inspect the origin, evidence and functional annotation of retrieved proteins and interactions, (iii) to visualize and adjust the resulting interaction network, (iv) to filter interactions based on method of derivation, evidence and type of experiment as well as based on gene expression data or gene lists and (v) to analyze the functional composition of interaction networks.

• Resource
• SciCrunch
• 17 years ago - by Anonymous

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

• Resource
• RRID-Legacy
• 6 years ago - by Anonymous

Core provides microbial sequencing, high-throughput nucleic acid extraction, microbial cultivation, and strain identification.

• Resource
• RRID
• 1 year ago - submitted by Edyta Vieth

The mission of the American Liver Foundation (ALF) is to facilitate, advocate and promote education, support and research for the prevention, treatment and cure of liver disease. These values guide our work as volunteers and staff of the American Liver Foundation as we move toward our ultimate goal of a world without liver disease. By living these values every day, we offer hope to all those affected by liver disease. * Research: Research is integral to the work of American Liver Foundation and is essential to improving treatment and finding cures. * Education: Many forms of liver disease are preventable, and many more can be cured if detected early. Yet tens of thousands of people in the U.S. are living with liver disease and don''t even know it. * Advocacy: American Liver Foundation takes a leadership role in advocating on behalf of the millions of Americans living with liver disease and their families.

• Resource
• SciCrunch
• 15 years ago - by Anonymous

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

• Resource
• RRID-Legacy
• 6 years ago - submitted by Fuxiang Wang

Core provides annotated biospecimens for basic, clinical, and translational research. Helps researchers access, collect, manage, and protect biospecimens using automated processes and quality control. Offers safe and monitored management of biospecimens including temperature-controlled storage, preparation of derivatives from these specimens, aliquoting, distribution, and production of specimen collection kits.

• Resource
• RRID
• 1 year ago - submitted by Edyta Vieth

Vector database is a digital collection of vector backbones assembled from publications and commercially available sources. This is a free resource for the scientific community that is compiled by Addgene. Only the plasmids deposited at Addgene are available for purchase through this website.

• Resource
• SciCrunch
• 15 years ago - by Anonymous