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Database of RNA-seq gene expression in hippocampal principal neurons. Hipposeq can analyze and visualize RNA-seq data for all excitatory cell populations in the hippocampus at multiple levels of granularity.

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• RRID-Legacy
• 9 years ago - submitted by Burak Ogan Mancarci

Provides fabrication services and consultations contributing to innovation in teaching, learning, research, and clinical care at the University of Pennsylvania.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Knowledge base (or ontology) that characterizes the state of current thought in cognitive science that captures knowledge from users with expertise in psychology, cognitive science, and neuroscience. There are two basic kinds of knowledge in the knowledge base. Terms provide definitions and properties for individual concepts and tasks. Assertions describe relations between terms in the same way that a sentence describes relations between parts of speech. The goal is to develop a knowledge base that will support annotation of data in databases, as well as supporting improved discourse in the community. It is open to all interested researchers. A fundamental feature of the knowledge base is the desire and ability to capture not just agreement but also disagreement regarding definitions and assertions. Thus, if you see a definition or assertion that you disagree with, then you can assert and describe your disagreement. The project is led by Russell Poldrack, Professor of Psychology and Neurobiology at the University of Texas at Austin in collaboration with the UCLA Center for Computational Biology (A. Toga, PI) and UCLA Consortium for Neuropsychiatric Phenomics (R. Bilder, PI). Most tasks used in cognitive psychology research are not identical across different laboratories or even within the same laboratory over time. A major advantage of anchoring cognitive ontologies to the measurement level is that the strategy for determining changes in task properties is easier than tracking changes in concept definitions and usage. The process is easier because task parameters are usually (if not always) operationalized objectively, offering a clear basis to judge divergence in methods. The process is also easier because most tasks are based on prior tasks, and thus can more readily be considered descendants in a phylogenetic sense.

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• SciCrunch
• 15 years ago - by Anonymous

Workflow software and methods language to improve the reproducibility of research results in the scientific community. The Aquarium Project aims to provide the means to specify, as precisely as possible, how to obtain a result using a combination of formal statements, informal descriptions, and photographs.

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• RRID-Legacy
• 9 years ago - submitted by Anita Bandrowski

Core utilizes dual tube micro X-ray computed tomography scanner for imaging specimens in fields of paleontology, comparative anatomy, evolution and development, basic biomedical studies, and research in geology and material sciences.It is equipped with 180 kV nano-focus and high power 240 kV micro-focus CT tube. This setup allows to scan very small specimens with high resolution using nano tube or dense fossils using high power tube.

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• SciCrunch
• 3 years ago - by Anonymous

Integrated public bioinformatics resource to support genomic, proteomic and systems biology research and scientific studies. Provides databases and protein sequence analysis tools to scientific community, including Protein Sequence Database which grew out from the Atlas of Protein Sequence and Structure. Conducts research in biomedical text mining and ontology, computational systems biology, and bioinformatics cyberinfrastructure. In 2002 PIR, along with its international partners, EBI (European Bioinformatics Institute) and SIB (Swiss Institute of Bioinformatics), were awarded a grant from NIH to create UniProt, a single worldwide database of protein sequence and function, by unifying the PIR-PSD, Swiss-Prot, and TrEMBL databases. Currently, PIR major activities include: i) UniProt (Universal Protein Resource) development, ii) iProClass protein data integration and ID mapping, iii) PRO protein ontology, and iv) iProLINK protein literature mining and ontology development. The FTP site provides free download for iProClass, PIRSF, and PRO.

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• SciCrunch
• 16 years ago - by Anonymous

Software for the analysis of short reads obtained from end-sequence RNA-seq. ESAT is designed for expression analysis of Digital expression (DGE) libraries that target transcript "ends."

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• RRID-Legacy
• 9 years ago - submitted by Anh Nguyet Vu

Core offers services, teaching and collaboration between Laser Processing Research Laboratory, Manufacturing Technology Research Laboratory and Bioenergy laboratory.

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• RRID
• 3 years ago - submitted by John Warren

Collaborative project to bring together biochemical pathway databases and research communities focused on plant metabolism. Used to build broad network of plant metabolic pathway databases. Central feature of PMN is PlantCyc, comprehensive plant biochemical pathway database, containing curated information from literature and computational analyses about genes, enzymes, compounds, reactions, and pathways involved in primary and secondary metabolism.

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• SciCrunch
• 17 years ago - by Anonymous

Portal used to coordinate activities of the German portion of the INCF group. The main focus is the development and free distribution of software tools for handling and analyzing neurophysiological data.

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• SciCrunch
• 17 years ago - by Anonymous

Software R package provides central location where curated data from experiments, publications or training courses can be accessed.

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• RRID
• 3 years ago - by Anonymous

Database for the diploid genome sequence of J. Craig Venter as published in PLoS Biology. Its graphical interface depicts the haploid sequence with SNP and insertion/deletion DNA variants as identified by genome assembly and comparison methods, as well as represents the haplotype blocks from which diploid genome sequence can be inferred and gene annotations.

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• SciCrunch
• 17 years ago - by Anonymous

Database to retrieve and compare gene expression patterns between animal species. Bgee first maps heterogeneous expression data (currently bulk RNA-Seq, scRNA-Seq, Affymetrix, in situ hybridization, and EST data) to anatomy and development of different species. Bgee is based exclusively on curated healthy wild-type expression data (e.g., no gene knock-out, no treatment, no disease), to provide a comparable reference of gene expression.

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• SciCrunch
• 17 years ago - by Anonymous

Web application for automated cell type annotation for scRNA-seq datasets. Allows for cell prediction using either built-in or custom models, in order to assist in accurate classification of different cell types and subtypes.

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• RRID
• 3 years ago - by Anonymous

Database of polymorphisms and mutations of the human mitochondrial DNA. It reports published and unpublished data on human mitochondrial DNA variation. All data is curated by hand. If you would like to submit published articles to be included in mitomap, please send them the citation and a pdf.

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• SciCrunch
• 17 years ago - by Anonymous

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 5th,2023. Core facility for the Emory Epithelial Pathobiology Research Development Center.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Database of mutations found in proteins involved in membrane-less organelles and liquid-liquid phase separation in human diseases.

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• RRID
• 3 years ago - by Anonymous

Software for fast and very memory-efficient calculation of isotope patterns, subsequent convolution to theoretical envelopes (profiles) plus valley detection and centroidization or intensoid calculation. Batch processing, resolution interpolation, wrapper, adduct calculations and molecular formula parsing.

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• SciCrunch
• 12 years ago - by Anonymous

Simulation software for experimental evolution of microorganisms. Aevol is a digital genetics model for the study of structural variations of the genome (e.g. number of genes, synteny, proportion of coding sequences).

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software application for network analysis and visualization of proteomics data. Cytoscape app that makes it easy to import STRING networks into Cytoscape, retains appearance and many of features of STRING, and integrates data from associated databases.

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• RRID
• 2 years ago - by Anonymous