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IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application.

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• RRID-Legacy
• 9 years ago - by Anonymous

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

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• RRID-Legacy
• 9 years ago - by Anonymous

CytoBackBone is an R package for merging of phenotype information from different cytometric profiles. Single-cell technologies are the most suitable techniques for the characterization of cells by the differential expression of the molecules that define their roles and functions in tissues. Among these techniques, mass cytometry represents a leap forward by increasing the number of available measurements to approximately 40 cell markers. Thanks to this technology, detailed immune responses were described in several diseases. However, the study of immune responses, such as that due to viral infections or auto-immune diseases, could be further improved by increasing the number of simultaneously measurable markers. To increase this number, we designed an algorithm, named CytoBackBone, which combines phenotypic information of different cytometric profiles obtained from different cytometry panels.

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• SciCrunch
• 9 years ago - submitted by Nicolas Tchitchek

Image reconstruction software for MRI. Its library provides common operations on multi-dimensional arrays, Fourier and wavelet transforms, as well as generic implementations of iterative optimization algorithms.

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• RRID-Legacy
• 9 years ago - by Anonymous

Virtual Slide Microscope Software by Olympus. This software will be read the data captured by VS120/cellSens. Images saved with VSI or Multi-Tiff file format can be read.

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• RRID-Legacy
• 9 years ago - by Anonymous

This pipeline and the included scripts are used to filter useful reads for SSPACE.

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• SciCrunch
• 9 years ago - submitted by Fu-Hao Lu

NGSimple (Next-Generation illumina SIMulation PipeLinE), mainly written in perl is designed to simulate NGS parameters (illumina sequencing type, read length, insert size and coverage) based on a given reference, and give a report to choose the best parameter combination that could contribute to a good assembly.

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• SciCrunch
• 9 years ago - submitted by Fu-Hao Lu

Standalone software tool for the integration of peptide identifications from mass spectrometry experiments into existing genome browser visualizations.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software that generates nucleotide, amino acid and codon sequence data by simulating insertions and deletions (indels) as well as substitutions. It is used for biological sequence simulation of multi-partitioned nucleotide, amino-acid, or codon data sets through the processes of insertion, deletion, and substitution in continuous time.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Open source software package for comparative sequence analysis using stochastic evolutionary models. Used for analysis of genetic sequence data in particular the inference of natural selection using techniques in phylogenetics, molecular evolution, and machine learning.

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Music composition and manipulation software.

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• RRID-Legacy
• 9 years ago - by Anonymous

The Alzheimer's Association created The Global Alzheimer's Association Interactive Network (GAAIN) to connect Alzheimer’s and dementia researchers and speed discovery by connecting potential collaborators to those sharing data (GAAIN Data Partners). GAAIN's powerful interactive tools allow users to explore data and create cohorts across multiple data sources and run immediate preliminary analysis while upholding the data control, security, and privacy policies of the data owners. These tools are freely accessible to all at www.gaaindata.org. A wide and vastly varying range of metadata from nearly 500,000 subjects can be explored using these tools. Attributes include demographics, assessments, health factors, biologicals, imaging and genetics.

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• NIF
• 9 years ago - submitted by Matt Travers

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data * and to select the best models in each locus.

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• SciCrunch
• 9 years ago - submitted by Luca Venturini

Web service for data exploration and analysis of the ABCD Study - the largest long-term study of brain development and child health in the United States.

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• SciCrunch
• 9 years ago - submitted by Edyta Vieth

Software package for signal-level analysis of Oxford Nanopore sequencing data.

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• SciCrunch
• 9 years ago - by Anonymous

Knowledge repository established to describe molecular mechanisms of Parkinson's Disease. It compiles literature-based information on PD into an easy to explore and freely accessible molecular interaction map and offers research-facilitating functionalities such as the overlay of experimental data and the identification of drug targets on the map

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• SciCrunch
• 9 years ago - submitted by Isabella Froman

Software repository holding a cloud-ready demonstration of the use of Kafka as a genomic database.

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• SciCrunch
• 9 years ago - submitted by Brendan Lawlor

Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.

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

Software that implements a framework to encode structural brain connectomes into multidimensional arrays (tensors). Encoding Connectomes provides an agile framework for computing over connectome edges and nodes.

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• NIF
• 9 years ago - submitted by Matt Travers

Data repository specifically focused on storage and dissemination of omic data generated from BRAIN Initiative and related brain research projects. Data repository and archive for BCDC and BICCN project, among others. NeMO data include genomic regions associated with brain abnormalities and disease, transcription factor binding sites and other regulatory elements, transcription activity, levels of cytosine modification, histone modification profiles and chromatin accessibility.

• SciCrunch
• 9 years ago - submitted by Anita Bandrowski