miRNAProtPred

FlowVision is offline flow cytometry analysis software for Windows and macOS. It supports FCS 2.0, 3.0, 3.1 and 3.2 file formats, polygon/rectangle/ellipse/quadrant gating with auto-fit (snap to cluster), spillover compensation, biexponential and hyperlog scales, MFI statistics (median, geometric mean, CV%), multi-file batch analysis with per-file gate overrides, and hierarchical gating. Spectral unmixing supports linear, NNLS, and Poisson-weighted least squares algorithms, with autofluorescence extraction and spillover spreading matrix. UMAP dimensionality reduction with reproducible seed and landmark mode for high-parameter panels. Imports FlowJo .wsp (compensation matrix) and exports gates to FlowJo .wsp and Gating-ML 2.0 (ISAC open standard) for interoperability with FlowJo, R/flowWorkspace/CytoML, and FCS Express.

An interactive platform that performs statistical analyses on metabolomics datasets and allows visualising results with ease. The interface gives users autonomy in creating figures suited to their reporting and publication needs.

A two-step desktop GUI application for RNA-seq differential gene expression (DEG) analysis. Step 1 reads raw GDC/TCGA STAR gene-count files together with a GDC sample sheet, matches samples to a Tumor/Normal design, and runs PyDESeq2 to produce normalized counts and DEG statistics. Step 2 generates publication-style volcano plots, MA plots, summary bar charts, and expression heatmaps (with optional gene labeling) from the results, exportable as PNG, PDF, SVG, or TIFF. Requires no coding from the user.

Plant Compound Extractor is a desktop application that builds a ready-to-use, deduplicated library of 3D ligand structures for a given plant. It queries multiple natural-product and chemical databases (COCONUT, LOTUS, Wikidata, PubChem, PlantaeDB, USDA Dr. Duke's, KNApSAcK and IMPPAT) in parallel, resolves each compound against PubChem for a canonical structure, and falls back to direct source retrieval when needed. Retrieved structures are then converted to 3D using RDKit, with configurable conformer generation and physicochemical filters (molecular weight, rotatable bonds, ring size, etc.). It can also process a manually supplied compound list, or convert an existing folder of 2D structures to 3D.

VigyanLLM is a sovereign, on-premises biomedical AI platform designed for computational biology. It provides autonomous primer design, evaluating melting temperature (Tm) and GC content; CRISPR guide RNA analysis with off-target scoring; BLAST sequence similarity searching; multiple sequence alignment (MSA); and GPU-accelerated molecular docking for drug discovery. Unlike cloud-based SaaS, VigyanLLM deploys via Docker to ensure institutional genomic data sovereignty

The Open Neuroscience Graph (openneuroscience.org) is an open-access, curated knowledge graph that maps the open science ecosystem in neuroscience as a browsable digital garden. Built from an Obsidian vault and published as a static website using Quartz, the project replaces traditional linear presentation with a networked structure of interlinked Markdown notes. Bidirectional links, full-text search, and an integrated graph visualization allow users to navigate thematic relationships dynamically rather than sequentially. The complete source material is openly available to sustain, replicate and extend the resource, includding all Markdown content, media attachments, Quartz configuration files, and site customizations. Researchers, educators, and open-science practitioners may explore the site directly, download the vault for offline use in Obsidian, or fork the material to build new, derivative knowledge bases. PID=https://doi.org/10.5281/zenodo.20181900