Curator Dashboard

The FP-CIT SPECT brain template has been created using a fully automatic procedure involving posterization of the source image to three levels: background, brain and striatum. We performed a spatial affine registration of these 40 posterized source images to a posterized reference image in the MNI space. The intensity values of the transformed images is normalized linearly, assuming that the histogram of the intensity values follows an alpha-stable distribution. Lastly, we built the [123I]FP-CIT SPECT template by the mean of the transformed and normalized images. More info: 1) Salas-Gonzalez et al. Building a FP-CIT SPECT brain template using a posterization approach. Accepted in Neuroinformatics. 2) Salas-Gonzalez et al. Linear intensity normalization of FP-CIT SPECT brain images using the alpha-stable distribution. NeuroImage, Volume 65, 2013, pp. 449-455. http://dx.doi.org/10.1016/j.neuroimage.2...

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• SciCrunch
• 12 years ago - submitted by Anita Bandrowski

Software program that simulates the evolution of nucleotide or amino acid sequences along a phylogeny using common models of the substitution process. A range of models of molecular evolution are implemented, including the general reversible model. State frequencies and other parameters of the model may be given and site-specific rate heterogeneity may also be incorporated in a number of ways. Any number of trees may be read in and the program will produce any number of data sets for each tree.

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• RRID-Legacy
• 10 years ago - by Anonymous

Simbios is the NIH Center for physics-based Simulation of Biological Structures. Simbios provides infrastructure, software, and training to help biomedical researchers understand biological form and function as they create novel drugs, synthetic tissues, medical devices, and surgical interventions. Simbios is investigating a wide scale of biological structures - from molecules to organisms. Driving biological problems include RNA folding, protein folding, myosin dynamics, cardiovascular dynamics, and neuromuscular biomechanics. Investigators interested in collaborating with Simbios can apply for NIH funding. To encourage collaboration in building accurate biological models and simulations, Simbios also provides the biomedical community with https://simtk.org, a free, secure, distributed, development system for projects. Projects may include models, software, data, documentation, publications, and graphics and have automatic backups and off-site storage. Projects may be public or private and have project-specific mailing lists, forums, bug & feature databases, news, blogs, and source-code repositories. Simbios is developing and disseminating the SimTK core simulation toolkit, (simtk.org/home/simtkcore). SimTK core is open-source software developed by experienced professionals. The software includes advanced capabilities for modeling the geometry and physics of biological systems. To ensure utility and accuracy, the software and training material is being developed and tested in close collaboration with biomedical scientists. Simbios has developed OpenSim, an application for advanced neuromuscular modeling that uses the SimTK toolkit, and is making it openly available at simtk.org/home/opensim. Simbios also publishes the Biomedical Computation Review, a magazine devoted to the science and tools in biocomputation, aimed at the community which encompasses the diverse biocomputation disciplines. To help researchers find high quality software and tools Simbios has also establishes the Simbiome an inventory of high-quality commercial and academic bio-simulation tools. Simbios has recurring openings for postdoctoral researchers.

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• SciCrunch
• 16 years ago - by Anonymous

The NeuroML database is a curated relational database that provides for the storage and retrieval of computational neuroscience models expressed in NeuroML, which is an extensible XML-based language for describing complex mathematical models of neurons and neuronal networks. NeuroML models are unique in their modular and multi-scale structure, where subcomponents of models can correspond to neuroscience models. In particular, the NeuroML database allows for efficient searches over the components of models and metadata that are associated with a hierarchical NeuroML model description.

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• SciCrunch
• 12 years ago - by Anonymous

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.

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• SciCrunch
• 13 years ago - by Anonymous

WordPress plugins for Anti-Spam, Metadata, Presentation, URLs, and Workflow from the Code4Lib community, a group of computer programmers and library technologists who largely work for and with libraries. Anti-Spam *Akimset - Filters out spam-link comments based on their content *reCAPTCHA - Requires users to copy a distorted word before they can comment Metadata *COinS Quicktags Button - In the non-WYSIWYG editor, can be used to build a basic COinS tag. This has been abandoned in favor of the generator at http://generator.ocoins.info/. *unAPI Server - Provides information about articles. Useful for Zotero users. Presentation *SyntaxHighlighter - Makes code pretty. *C4LJ Custom the_author()- Replaces the text returned by the_author() with the value of the author custom field. Necessary since articles are entered by their editors, but we want author information to appear on the articles and in the syndication feeds. URLs *C4LJ Remove Parents - A customization of http://wordpress.org/extend/plugins/remove-parents/. Prettifies category URLs so that issues appear at http://journal.code4lib.org/issues/issue1 instead of http://journal.code4lib.org/issues/issues/issue1. *FeedBurner FeedSmith - Redirects the main feed and the general comments feed to FeedBurner Workflow *Issue Manager - Enables one-click publishing of new issues, and prevents articles from being published until their associated issue is published. *Role Manager - Allows creation of custom roles and editing of roles' permissions. Used to create the Reviewer role, which can read Private articles, so that authors can see their articles before publication, and to prevent editors from publishing articles on accident.

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• SciCrunch
• 17 years ago - by Anonymous

A non-governmental wildlife research institution involved in the conservation of nature, primarily biological diversity and threatened species through action based on research, education and public awareness. Contains publications, collections, and educational materials as well as information on current research.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software performing alignment of high-throughput RNA-seq data. Aligns RNA-seq reads to reference genome using uncompressed suffix arrays.

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• SciCrunch
• 13 years ago - by Anonymous

Community built database about RNA / DNA or Peptide aptamers. The Aptamer Base is a collaborative knowledge base about aptamers, their interactions and detailed experimental conditions with citations to primary scientific literature. Aptamers are short single-stranded nucleic acids or amino acid polymers that recognize and bind to targets with high affinity and selectivity. Nucleic acid aptamers are typically isolated from large combinatorial libraries through the application of SELEX. For more information visit http://aptamerbase.semanticscience.org

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• SciCrunch
• 15 years ago - by Anonymous

An institution which serves as a deposit of saprotrophic ascomycete and zygomycete strains. 3400 isolates are contained, 2400 of which are available to the public. The collection also provides atlases of each. While some strains are provided for free, other services, such as providing strains for teaching or research or identifying cultures, are provided for a charge.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

THIS TEST is a

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• NIF
• 3 years ago - by Anonymous

A virtual database that indexes both BioNOT for negation data, and the Resource Discovery Pipeline: an automated resource discovery and semi-automated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. This virtual database currently indexes the following resources: * BioNOT, http://snake.ims.uwm.edu/bionot/index.php?searchterm=mecp2+autism&submit=Search * Resource Discovery Pipeline, http://lucene1.neuinfo.org/nif_resource/current/

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• SciCrunch
• 14 years ago - by Anonymous

A database providing information about compounds under investigation for therapeutic use. There are currently 44 compounds on record with 100 compounds in the process of being uploaded to the database.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Provides latests technologies for stem cell biology, stem cell differentiation, organoid formation and induced pluripotent stem cells.Tissue Engineering platform works in collaboration with Biomolecular Screening and Protein Technologies Unit to provide CRISPR/Cas9 genome editing technology service.Unit also includes Histology In-house Service (only for PRBB residents) provides histopathological analysis required for analysing tissues from research performed in in vivo models. Histology In-house Service performs and optimizes histological processing and analysis of tissue, from experimental animal models and human origin.Provides mentoring and training in common histological techniques.

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• SciCrunch
• 3 years ago - submitted by Edyta Vieth

Centre is committed to free and open exchange of scientific data and is working collaboratively with international centres, networks and scientists to build sustainable polar data commons. Delivers professional data management and analysis services to Antarctic scientists and environmental managers. Supports logistical operations of Australian Antarctic Program. Data held in AADC data stores are qualified with metadata and discoverable through Catalogue of Australian Antarctic and Sub-antarctic Metadata (CAASM http://data.aad.gov.au/aadc/metadata) or through customized applications accessible via the website. All data is archived in AADC to permit its re-use. AADC has capability to create DOIs for datasets.

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• SciCrunch
• 14 years ago - by Anonymous

A portal for malaria researchers and professionals. The site provides links to articles, news, discussion forums, the MalariaWorld journal, weblogs, events, and job listings.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

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.

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• SciCrunch
• 13 years ago - by Anonymous

Growing library of software for physiologic signal processing and analysis, detection of physiologically significant events using both classical techniques and novel methods based on statistical physics and nonlinear dynamics, interactive display and characterization of signals, creation of new databases, simulation of physiologic and other signals, quantitative evaluation and comparison of analysis methods, and analysis of nonequilibrium and nonstationary processes. A unifying theme of the research projects that contribute software to PhysioToolkit is the extraction of hidden information from biomedical signals, information that may have diagnostic or prognostic value in medicine, or explanatory or predictive power in basic research. Contributions of software to PhysioToolkit are welcome, http://physionet.org/guidelines.shtml#software-contributions

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• SciCrunch
• 14 years ago - by Anonymous

A repository which hosts and archives original and edited scientific papers. Scientists can post their academic manuscripts on Libre, where they can find reviewers who will formally evaluate the manuscripts. Evaluated works are posted alongside the original manuscript with reviewers' identities disclosed and the work they edit given its own DOI. Users can post additional updated versions of their work to Libre or send their papers to journals. Papers and reviews are rated by other scientists, and from these Libre creates holistic indeces listing the best rated writers and reviewers.

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• SciCrunch
• 12 years ago - submitted by Kristen Jensen

Software collection of libraries and applications implementing large parts of DICOM standard for medical image communication.Includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over network connection, as well as demonstrative image storage and worklist servers.

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• SciCrunch
• 17 years ago - by Anonymous