Curator Dashboard

Software tool for BUSCO compilation and comparison. Used for assessing completeness in multiple genome assemblies.Used for assembly comparison designed to be robust to differences in assembly size and base calling quality.

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• SciCrunch
• 5 years ago - submitted by Richard Edwards

Software tool for read-depth based genome size prediction. Wrapper for genome size estimate methods of Diploidocus.Uses long read depth of coverage and BUSCO single copy orthologue prediction to estimate genome size.

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• SciCrunch
• 5 years ago - submitted by Richard Edwards

Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly.

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• SciCrunch
• 5 years ago - submitted by Richard Edwards

Publicly available, searchable, data resource that aims to increase transparency, reproducibility and translatability of preclinical efficacy studies of candidate therapeutics for Alzheimer’s disease. Knowledge platform for dissemination of data and analysis to scientists, from academic centers, industry, disease focused foundations. Provides quick access and visibility to integrated preclinical efficacy data from published and unpublished studies.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Software tool designed by Data Coordination Platform of Human Cell Atlas to process single-cell RNAseq data generated by Smart-seq2 assays.Processes stranded or unstranded, paired- or single-end, scRNA-seq data from an individual cell.

• Resource
• SciCrunch
• 5 years ago - submitted by Elizabeth Kiernan

Software tool as spatial analysis software for whole tissue sections.Utilizes information on cell type and position to phenotype local neighborhoods and reveal how their spatial distribution leads to generation of global tissue architecture.Used to make advanced data analytic techniques accessible for single cell data with position information.

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• RRID-Legacy
• 5 years ago - by Anonymous

Open source software tool as 3D finite element grid generator with build in CAD engine and post processor. Provides meshing tool with parametric input and advanced visualization capabilities. Built around geometry, mesh, solver and post processing modules.Specification of any input to these modules is done either interactively using graphical user interface, in ASCII text files using Gmsh own scripting language (.geo files), or using C plus plus, C, Python or Julia Application Programming Interface.

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• RRID-Legacy
• 5 years ago - by Anonymous

Evidence Graph Ontology extends core concepts from W3C Provenance Ontology PROV-O to describe evidence for correctness of findings in biomedical publications. Semantic data model in EVI is expressed using OWL2 Web Ontology Language.

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• dkNET
• 5 years ago - submitted by Maryann Martone

General purpose, document based, distributed database built for modern application developers and for the cloud. Offers Community and Enterprise version of database.MongoDB Community is source available and free to use edition of MongoDB. MongoDB Enterprise is available as part of MongoDB Enterprise Advanced subscription and includes comprehensive support for your MongoDB deployment. MongoDB Enterprise also adds enterprise-focused features such as LDAP and Kerberos support, on-disk encryption, and auditing.MongoDB also offers Atlas,hosted MongoDB Enterprise service option in cloud which requires no installation overhead and offers free tier to get started.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Software tool as knowledge graph platform to create flexible, reusable data layer for answering complex queries across data silos. Used for organizing data to highlight relationships between data points. Unifies data based on its meaning, creating connected network of knowledge.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Open source identity and access management solution written in Java. Offers features such as Single-Sign-On, Identity Brokering and Social Login, User Federation, Client Adapters, Admin Console, and Account Management Console by WildFly, a division of Red Hat.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Software tool based on open source solutions to make deploying microservices easy. Used for deployment of modern IT environments. Allows to expose applications to network in dynamic environment.Traefik Stack by Traefik Labs Inc. as cloud native stack to help enterprises manage their entire network across data centers, on-premises servers and public clouds.Tools options include Traefik Proxy,Traefik Enterprise,Traefik Mesh,Traefik Pilot.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Software tool as reusable computational framework, enabling simplified access to modern scalable cloud based components. Implements FAIR data principles and extends them to provide fully FAIR Evidence, including machine interpretable provenance of datasets, software and computations, as metadata for all computed results.All objects are assigned persistent IDs, including software.

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• dkNET
• 5 years ago - submitted by Maryann Martone

Software pipeline that supports processing of multiplexed single nuclei bisulfite sequencing data to detect methylated bases. Alignment and methylated base calling pipeline that trims adaptors, attaches cell barcodes, aligns reads to genome, filters reads based on quality and creates both VCF and ALLC file with Emethylation site coverage.

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• RRID-Legacy
• 5 years ago - submitted by Elizabeth Kiernan

Software tool for modelling RNA binding protein binding preferences. Used to predict RPB binding sites. Computational RBP binding site prediction framework based on recurrent neural networks. Includes functionalities from dataset generation over model training to evaluation of binding preferences and binding site prediction.

• Resource
• SciCrunch
• 5 years ago - submitted by Michael Uhl

Behavioral two photon imaging system. Includes two photon scanning microscope, software and virtual reality set up. Used for chronic two photon imaging in mice exploring virtual environment. Tool in neuroscience to allow for chronic measurement of activity of genetically identified cells during behavior.

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• RRID-Legacy
• 5 years ago - submitted by Felix Widmer

Open source game engine and framework for 3D rendering and game development for Python and C++ programs. Graphics engine and programming environment to support everything from real time graphics applications to development of high end virtual reality theme park attractions or video games.

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• RRID-Legacy
• 5 years ago - submitted by Felix Widmer

Portal for cross sectional study where population based sample of adult cancer patients were recruited for mailed survey (with telephone follow-up of non-responders) to evaluate equivalence of PROMIS measures across socio-demographic and clinical sub-groups.

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• RRID-Legacy
• 5 years ago - by Anonymous

Data repository for Friedrich Miescher Institute for Biomedical Research in areas of epigenetics, quantitative biology, and neurobiology.

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• RRID-Legacy
• 5 years ago - submitted by Felix Widmer

Software package for image processing for MATLAB. Used for processing of calcium imaging data.

• Resource
• RRID-Legacy
• 5 years ago - submitted by Felix Widmer