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https://team.inria.fr/empenn/research/

Research team focused on research and development of new algorithms in medical imaging, information processing and computer assisted intervention in the context of the pathologies of the central nervous system. Research team jointly affiliated to INSERM (National Institute of Health and Scientific Research), Inria (National Institute of Research in Computer Sciences and Automation) and IRISA / UMR CNRS 6074, University of Rennes I. Multidisciplinary team merging researchers in image processing and medical doctors.

Proper citation: VISAGES Research (RRID:SCR_000749) Copy   

•   Source: SciCrunch Registry

http://www.flybrain.org/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Interactive database of Drosophila melanogaster nervous system. Used by drosophila neuroscience community and by other researchers studying arthropod brain structure.

Proper citation: FlyBrain (RRID:SCR_000706) Copy   

•   Source: SciCrunch Registry

http://www.aniseed.cnrs.fr/

Database of ascidian embryonic development at the level of the genome (cis-regulatory sequences, gene expression, protein annotation), of the cell (morphology, fate, induction, lineage) or of the whole embryo (anatomy, morphogenesis). Currently, four organism models are described in Aniseed: Ciona intestinalis, Ciona savignyi, Halocynthia roretzi and Phallusia mammillata.
This version supports four sets of Ciona intestinalis transcript models: JGI v1.0, KyotoGrail 2005, KH and ENSEMBL, all functionally annotated, and grouped into Aniseedv3.0 gene models. Users can explore their expression profiles during normal or manipulated development, access validated cis-regulatory regions, get the molecular tools used to assay gene function, or all articles related to the function, or regulation of a given gene. Known transcriptional regulators and targets are listed for each gene, as are the gene regulatory networks acting in individual anatomical territories.
ANISEED is a community tool, and the direct involvement of external contributors is important to optimize the quality of the submitted data. Virtual embryo: The 3D Virtual embryo is available to download in the download section of the website.

Proper citation: Ascidian Network for InSitu Expression and Embryological Data (RRID:SCR_013030) Copy   

•   Source: SciCrunch Registry

http://www.bioeng.nus.edu.sg/compbiolab/projects/index.html

The Computational Bioengineering Laboratory in the Division of Bioengineering at the National University of Singapore has expertise in mathematical modeling, software and algorithm development, numerical techniques such as finite element analysis, computer simulation and visualization, signal and image processing plus an understanding of the biological systems that drive our efforts. The following are the main themes underlying the Computational Bioengineering Laboratory projects: - Computational Biology - Computational Physiology - Biosignal & Bioimage Processing - Integrated Physiology & the Physiome Project

Proper citation: National University of Singapore, Computational Bioengineering Laboratory (RRID:SCR_000284) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/MapE15_5_01.htm

Abbreviated reference atlas for the Embryonic 15.5 post conception day mouse. All sections were nissl stained and digitized. To assist in the initial identification of sites of gene expression sites, maps of brains are available for E15.5, P7 and the adult. These maps depict the boundaries of major brain regions (cortex, thalamus, striatum, globus pallidus, ventral striatum, septum, basal forebrain, hippocampus, midbrain, pons, medulla, cerebellum) and also show the more prominent nerve tracts. Maps are most efficiently used by placing the window depicting the map of interest next to the gene expression image. Browsing between planes of sectioning is permitted thus allowing the most appropriate plane to be selected. The annotation of anatomical details such as brain nuclei is currently beyond the scope of the GenePaint database. Hence, such information on the anatomy of the brain and embryo should be obtained from published atlases of mouse anatomy (Kaufman, 1995; Paxinos and Franklin, 2001; Jacobowitz and Abbott, 1997; Schambra et al., 1992; Valverde1998).

Proper citation: GenePaint E15 Atlas (RRID:SCR_002786) Copy   

•   Source: SciCrunch Registry

http://www.cnbc.cmu.edu/

CNBC is joint venture of University of Pittsburgh and Carnegie Mellon University. Our center leverages the strengths of the University of Pittsburgh in basic and clinical neuroscience and those of Carnegie Mellon in cognitive and computational neuroscience to support a coordinated cross-university research and educational program of international stature. In addition to our Ph.D. program in Neural Computation, we sponsor a graduate certificate program in cooperation with a wide variety of affiliated Ph.D. programs.

Proper citation: Center for the Neural Basis of Cognition (RRID:SCR_002301) Copy   

•   Source: SciCrunch Registry

http://embryo.soad.umich.edu/animal/home.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on February 14, 2013. A multidimensional, digital atlas based on magnetic resonance images of normal mouse embryos from 9.5 days after conception (E9) to the newborn (P0). The images include surface views and cross-sectional views from the transverse, coronal, and sagittal planes for each embryo. Several movies have also been included to demonstrate growth of the embryos and to present a variety of visualization tools available for studying and documenting embryonic anatomy. These images are organized as a reference for educators and researchers who want to understand better the embryological anatomy of their own specimens and to understand how their images relate to the whole embryo at many stages of development.

Proper citation: Magnetic Resonance Microscopy of Mouse Embryo Specimens (RRID:SCR_001145) Copy   

•   Source: SciCrunch Registry

http://www.alspac.bris.ac.uk

A long-term health research project which follows pregnant women and their offspring in a continuous health and developmental study. More than 14,000 mothers enrolled during pregnancy in 1991 and 1992, and the health and development of their children has been followed in great detail. The ALSPAC families have provided a vast amount of genetic and environmental information over the years which can be made available to researchers globally.

Proper citation: ALSPAC (RRID:SCR_007260) Copy   

•   Source: SciCrunch Registry

http://www.usc.edu/schools/medicine/research/institutes/igm/cpihd/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. CPIHD is a novel Center that blends research and outreach targeting preterm infants and their families. Faculty of the Center work together to find solutions to the complex biomedical, psychological, and social problems associated with preterm delivery. The Center for Premature Infant Health and Development goals are to: discover the causes of health and developmental problems encountered by preterm infants; develop and disseminate optimal family-centered prevention, assessment, and intervention strategies to improve long-term outcomes for preterm infants and families; and eliminate racial disparities in adverse birth outcomes in our community. The missions of CPIHD are: conducting interdisciplinary, translational, and family-centered research; educating the next generation of researchers and practitioners serving preterm infants and their families; and providing community-based outreach to serve families of, and health care workers caring for, preterm infants.

Proper citation: Center for Premature Infant Health and Developement (RRID:SCR_008074) Copy   

•   Source: SciCrunch Registry

http://www.genepaint.org/R0_1.htm

A digital atlas of gene expression patterns in the mouse. Expression patterns are determined by non-radioactive in situ hybridization on serial tissue sections. An accompanying atlas based on maps of sagittal sections at embryonic day 14.5. E14.5 NMRI embryo was prepared, sectioned and imaged identically to the embryos used for in situ hybridization. Maps are accessed from the set viewer page using the appropriate button above the image directory. Both, the in situ hybridization section and the appropriate atlas section can be viewed side-by-side. Section thickness is 20 m and inter-section distance is 100 m. Tissue was stained with cresyl violet (Nissl-method). All sections were digitally scanned using a 5x objective. Structures annotated for gene expression are indicated in the maps with red pointers. Boundaries between brain regions are indicated with dashed yellow lines.

Proper citation: GenePaint Interactive Anatomy Atlas (RRID:SCR_007680) Copy   

•   Source: SciCrunch Registry

http://www.aiddata.org/

Portal of information about international economic development assistance, dating back to 1947, that includes a database of nearly one million past and present aid activities around the world, aid information management services and tools, data visualization technologies, and research designed to increase understanding of development finance. AidData is searchable by topic such as disaster prevention, energy supply, water supply or reconstruction relief. You may also search by specific regions including Africa, Europe, America, Asia, or Oceania.

Proper citation: AidData (RRID:SCR_010480) Copy   

•   Source: SciCrunch Registry

https://www.mcdb.ucla.edu/Research/Hartenstein/dbla/index.html

Atlas providing structure and development of Drosophila brain lineages. Used to learn about projection pattern of lineages as first step towards reconstructing and understanding all neurons.

Proper citation: Drosphila Brain Lineage Atlas (RRID:SCR_017507) Copy   

•   Source: SciCrunch Registry

https://brads.nichd.nih.gov/Home/

Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data.

Proper citation: Biospecimen Repository Access and Data Sharing (RRID:SCR_017383) Copy   

•   Source: SciCrunch Registry

http://www.creative-diagnostics.com/

An antibody supplier that also provides diagnostic components, assay reagents and contract biologic RandD and manufacturing services. The company focuses on providing services to help clients develop, manufacture and commercialize their products.

Proper citation: Creative Diagnostics (RRID:SCR_000367) Copy   

•   Source: SciCrunch Registry

http://kb.phenoscape.org/

Knowledgebase that uses ontologies to integrate phenotypic data from genetic studies of zebrafish with evolutionary variable phenotypes from the systematic literature of ostariophysan fishes. Users can explore the data by searching for anatomical terms, taxa, or gene names. The expert system enables the broad scale analysis of phenotypic variation across taxa and the co-analysis of these evolutionarily variable features with the phenotypic mutants of model organisms. The Knowledgebase currently contains 565,158 phenotype statements about 2,527 taxa, sourced from 57 publications, as well as 38,189 phenotype statements about 4,727 genes, retrieved from ZFIN. 2013-01-26.

Proper citation: Phenoscape Knowledgebase (RRID:SCR_002821) Copy   

•   Source: SciCrunch Registry

http://www.wormatlas.org/

Anatomical atlas about structural anatomy of Caenorhabditis elegans. Provides simple interface allowing user to easily navigate through every anatomical structure of worm. Contains set of images which can be sorted by different characteristics: sex, genotype, age, body portion or tissue type. Includes links to other major worm websites and databases. Application for viewing and downloading thousands of unpublished electron micrographs and associated data. These images have been generated by several labs in the C. elegans community, including the MRC, the Hall lab (Center for C. elegans Anatomy), and the Culotti and Riddle labs.

Proper citation: WormAtlas (RRID:SCR_002861) Copy   

•   Source: SciCrunch Registry

http://magest.hgc.jp/

A database for maternal gene expression information for ascidia, colloquially known as sea squirts. Information available includes DNA sequences, expression patterns of ESTs, and cDNA data from uncleaved fertilized eggs. The goal is to utilize the database to understand molecular mechanisms of establishment of embryonic body plans of chordates and to understand evolution from invertebrates to vertebrates in the future.

Proper citation: MAboya Gene Expression Patterns and Sequence Tags (RRID:SCR_000763) Copy   

•   Source: SciCrunch Registry

http://chordate.bpni.bio.keio.ac.jp/faba/1.4/top.html

Image resource including ascidian's three-dimensional (3D) and cross-sectional images through the developmental time course. These images were reconstructed from more than 3,000 high-resolution real images collected by confocal laser scanning microscopy (CLSM) at newly defined 26 distinct developmental stages (stages 1-26) from fertilized egg to hatching larva, which were grouped into six periods named the zygote, cleavage, gastrula, neurula, tailbud, and larva periods. The data set will be helpful in standardizing developmental stages for morphology comparison as well as for providing guidelines for several functional studies of a body plan in chordate.

Proper citation: Four-dimensional Ascidian Body Atlas (RRID:SCR_001691) Copy   

•   Source: SciCrunch Registry

https://www.bgee.org/

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.

Proper citation: Bgee: dataBase for Gene Expression Evolution (RRID:SCR_002028) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/swissprot/hpi/hpi.html

THIS RESOURCE IS NO LONGER IN SERVICE, documented on August 03, 2011. IT HAS BEEN REPLACED BY A NEW UniProtKB/Swiss-Prot ANNOTATION PROGRAM CALLED UniProt Chordata protein annotation program. The Human Proteome Initiative (HPI) aims to annotate all known human protein sequences, as well as their orthologous sequences in other mammals, according to the quality standards of UniProtKB/Swiss-Prot. In addition to accurate sequences, we strive to provide, for each protein, a wealth of information that includes the description of its function, domain structure, subcellular location, similarities to other proteins, etc. Although as complete as currently possible, the human protein set they provide is still imperfect, it will have to be reviewed and updated with future research results. They will also create entries for newly discovered human proteins, increase the number of splice variants, explore the full range of post-translational modifications (PTMs) and continue to build a comprehensive view of protein variation in the human population. The availability of the human genome sequence has enabled the exploration and exploitation of the human genome and proteome to begin. Research has now focused on the annotation of the genome and in particular of the proteome. With expert annotation extracted from the literature by biologists as the foundation, it has been possible to expand into the areas of data mining and automatic annotation. With further development and integration of pattern recognition methods and the application of alignments clustering, proteome analysis can now be provided in a meaningful way. These various approaches have been integrated to attach, extract and combine as much relevant information as possible to the proteome. This resource should be valuable to users from both research and industry. We maintain a file containing all human UniProtKB/Swiss-Prot entries. This file is updated at every biweekly release of UniProt and can be downloaded by FTP download, HTTP download or by using a mirroring program which automatically retrieves the file at regular intervals.

Proper citation: Human Proteomics Initiative (RRID:SCR_002373) Copy   

•   Source: SciCrunch Registry