Curator Dashboard

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18, 2020. Software package to create, visualize and analyze biological networks. Can include coding relations to distinguish between genes and their products. BisoGenet client is designed to work as Cytoscape plugin for querying server along with graph topology analysis and visualization options for easing interpretation process.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

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.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

Software tool as flexible and comprehensive codon usage analyzer. Used to analyze codon usage bias (CUB) and relevant problems.

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• 6 years ago - submitted by Nathan Anderson

Sequential B-Cell Epitope Predictor. Web server predicts B-cell epitopes from protein sequence. Sequence-based B-cell epitope prediction using conformational epitopes. Sequences of protein of interest should be in fasta format. BepiPred 2.0 is available as stand alone software package, with same functionality as web service., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• 6 years ago - submitted by Nathan Anderson

Web tool that automatically screens bioRxiv preprints for rainbow colormaps, which are not colorblind safe. Emails authors information on replacing these colormaps with colorblind safe alternatives. Screens preprints to improve data representation and colour-blind accessibility.

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• RRID-Legacy
• 6 years ago - submitted by Tracey Weissgerber

Software suite that works by themselves, and with Amber20 itself. Can be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models.

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• SciCrunch
• 6 years ago - submitted by Nathan Anderson

Web server for in silico prediction of allergens. Alignment free server for in silico prediction of allergens based on main physicochemical properties of proteins. Used to predict the route of allergen exposure: food, inhalant or toxin.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.

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• RRID-Legacy
• 6 years ago - submitted by Nathan Anderson

Quick and intuitive way to annotate data from genomics studies including microbiome. Project to aid researchers in applying standardized metadata describing what, where, how, and when of samples collected in genomics study. Collection of METAdata of GEnomics studies on web based NOTEbook. Metadata are stored in centralized repository and validated according to guidelines from Genomics Standard Consortium, which are also supported by repositories and large microbiome initiatives such as NCBI, European Bioinformatics Institute (EBI), and Earth Microbiome Project. Upon request from researchers, data will also be submitted for publication via NCBI Sequence Read Archive (SRA) repository.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Software text mining tool aiding curation at Rat Genome Database. Ontology driven, concept based literature search engine developed at RGD. Tags abstracts with gene names, gene mutations, organism names and terms from ontologies vocabularies used at RGD. Open and fully customizable.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Open knowledge base that can be read and edited by both humans and machines. Storage for structured data of its Wikimedia sister projects including Wikipedia, Wikivoyage, Wiktionary, Wikisource, and others. Provides support to many other sites and services beyond just Wikimedia projects.

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• SciCrunch
• 6 years ago - submitted by Pascal Welke

Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.

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• RRID-Legacy
• 6 years ago - by Anonymous

Comprehensive database of A-to-I RNA Editing Events. Atlas of A-to-I RNA editing events in human and other organisms. Collection of A-to-I events in body sites of healthy individuals from GTEx project. RNA Editing sites can be searched by genomic region, gene name and other relevant features as tissue of origin. Query results are shown in sortable and downloadable tables in which main characteristics of individual RNA editing events are reported. RNA-Seq and DNA-Seq coverage per site as well as RNA editing levels are provided.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

The PureLink RNA Mini Kit is a column-based kit used to isolate high-quality total RNA from a wide variety of sample types in 20 minutes using standard laboratory equipment. The kit includes RNase-free lysis and wash solutions that protect RNA from RNases while liberating the RNA from DNA, proteins, and other cellular debris. The fast spin-column workflow is ideal for processing low to mid-throughput batch sizes. The advanced PureLink RNA Mini spin column design allows for maximum sample input (200 mg of tissue) and RNA recovery (up to 1000 µg). This means that users can process both small and large sample sizes with the same RNA isolation kit.

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• 6 years ago - submitted by Lucia Garcia del Valle

Cell Line Adenosine-to-Inosine RNA editing database. Searchable catalogue of RNA editing levels across cell lines. Used to facilitate rational choice of appropriate cell lines for future work on A-to-I RNA editing.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

The SuperScript VILO cDNA Synthesis Kit is designed to generate first strand cDNA for two-step RT-qPCR applications. The kit is supplied in a 2-tube format with the VILO Reaction Mix and an enzyme blend in separate tubes. The enzyme blend contains SuperScript III Reverse Transcriptase (RT), a genetically engineered MMLV RT that has reduced RNase H activity and improved thermostability for highly efficient cDNA synthesis. The kit can be used to synthesize cDNA from for a wide range of input RNA amounts.

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• RRID-Legacy
• 6 years ago - submitted by Lucia Garcia del Valle

Software tool as big image data compatible Fiji plugin for trainable image segmentation.

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• 6 years ago - submitted by Lucia Garcia del Valle

Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.

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• dkNET
• 6 years ago - submitted by Ko-Wei Lin

Software tool for visual inspection and processing of big image data. Enables loading of Tiff and Hdf5 based image data. BDC supports cropping and saving of big image data including binning and bit depth conversion. Used for analysis of TB sized image data like light sheet microscopy or electron microscopy.

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• RRID-Legacy
• 6 years ago - submitted by Lucia Garcia del Valle

AllStars Negative Control siRNA is the most thoroughly tested and validated negative control siRNA currently available. This siRNA has no homology to any known mammalian gene. Validation has been performed using Affymetrix GeneChip arrays and a variety of cell-based assays to ensure minimal nonspecific effects on gene expression and phenotype. Minimal nonspecific effects ensure that comparison of the gene-specific siRNA to the negative control gives a true picture of the effects of target-gene knockdown on gene expression and phenotype. If the negative control causes nonspecific effects then results from RNAi experiments can be misleading and difficult to interpret. Cloning experiments confirmed that AllStars Negative Control siRNA enters RISC. AllStars Negative Control siRNA is patent-pending and the sequence is proprietary.

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• RRID-Legacy
• 6 years ago - submitted by Arindam Dey