Programming
Software development: programming languages, coding, libraries and frameworks, software engineering and architecture, source control, developer tools, databases, and infrastructure.
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Quarto Dashboards video series opensource.posit.co
A three-part video series covering first dashboards, dashboard components, and theming and styling, with slides and starter code for R and Python, by Mine Çetinkaya-Rundel.
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Collaborating on Quarto documents nrennie.rbind.io
A blog post outlining several options for collaborating on Quarto documents with non-technical collaborators who do not want to edit code, covering both Git-based and Git-free workflows by Nicola Rennie.
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How to publish your Quarto document/book/website as a Docker container? mickael.canouil.fr
A blog post describing how to publish your Quarto document/book/website as a Docker container by Mickaël Canouil.
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Quarto for the Python User jumpingrivers.com
A blog post introducing Quarto to Python users for creating reports.
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Quarto dashboard creation and automation ivelasq.rbind.io
A blog post on building a dashboard that pulls data from an API, pins it, and republishes on a schedule, by Isabella Velásquez.
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A beginner's guide to using Observable JavaScript, R, and Python with Quarto infoworld.com
This article shows you how to set up a Quarto document to use Observable JavaScript, including how to pass data from R or Python to an Observable code chunk.
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Quarto GitLab CI/CD component gitlab.com
A reusable GitLab CI/CD component that renders and publishes Quarto projects to GitLab Pages.
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Albert Rapp (@AlbertRapp) github.com
Publishes Quarto blogging, Typst, and web development tutorials via his blog and newsletter (BlueSky: @albertrapp.bsky.social).
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ggsegverse ggsegverse.github.io
Website for the ggsegverse R package ecosystem for brain-segmentation visualisation, with custom theming and JavaScript integration with the r-universe API.
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Tutorial: Quarto for Reproducible Research Workflows and Academic Publishing elenlefoll.quarto.pub
An open educational resource covering literate programming, reproducibility, and multi-format publishing for academic writing by Elen Le Foll.
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We don't talk about Quarto apreshill.com
A blog post introducing Quarto publishing software by Alison Presmanes Hill.
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LeafByte zoegp.science
Free and open source mobile app for measuring herbivory quickly and accurately.
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QuPath qupath.github.io
Open source software for digital pathology image analysis.
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RhizoTrak prbio-hub.github.io
Open source tool for flexible and efficient manual annotation of complex time-series minirhizotron images.
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Orbit orbit.bio
A versatile image analysis software for biological image-based quantification using machine learning, especially for whole slide imaging.
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Tutorial: Personal Website using Jupyter Notebook and Quarto adtarie.net
A Python-oriented step-by-step tutorial on how to create a website using Quarto.
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MorphoGraphX morphographx.org
Open source application for the visualization and analysis of 4D biological datasets.
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Biobeam maweigert.github.io
Open source software package that is designed to provide fast methods for in-silico optical experiments with an emphasize on image formation in biological tissues.
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PAT-GEOM ianzwchan.com
A software package for the analysis of animal colour pattern.
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Icy github.com
Open community platform for bioimage informatics, providing software resources to visualize, annotate and quantify bioimaging data.
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A Hitchhiker's guide through the bio-image analysis software universe febs.onlinelibrary.wiley.com
An article presenting a curated guide and glossary of bio-image analysis terms and tools.
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Biological imaging software tools dx.doi.org
The steps of biological image analysis and the appropriate tools for each step.
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BacStalk drescherlab.org
Interactive and user-friendly image analysis software tool to investigate the cell biology of common used bacterial species.
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PyScratch bitbucket.org
Open source tool that autonomously performs quantitative analysis of in vitro scratch assays.
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BiaPy biapyx.github.io
Open source ready-to-use all-in-one library that provides deep-learning workflows for a large variety of bioimage analysis tasks.
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Vaa3D alleninstitute.org
Open-source software for 3D/4D/5D image visualization and analysis.
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Stream data from ChatGPT with JavaScript umaar.com
Learn how to consume streaming data from ChatGPT using vanilla JavaScript.
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16x Prompt prompt.16x.engineer
Cross-platform app to add source code and formatting instructions into prompt for coding tasks. ($)
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Price Per Token pricepertoken.com
Compare LLM API pricing across providers. Includes token counter and cost calculator.
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Sidekick github.com
Connect external data to ChatGPT APIs through a dashboard.
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Developer Duck apps.apple.com
Native developer-focused macOS app with Xcode plugin and command line support. ($)
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The Haskell Tool Stack docs.haskellstack.org
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ZINC ligand discovery database zinc.docking.org
Free database of commercially-available compounds for virtual screening.
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WikiPathways wikipathways.org
Database of biological pathways.
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UniRef uniprot.org
Non-redundant sequence database clustering UniProtKB entries at multiple sequence identity thresholds.
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UniProt REST API uniprot.org
Programmatic access to protein sequence and functional annotation data.
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Uniclust uniclust.mmseqs.com
Clustered protein sequence databases.
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Squidpy squidpy.readthedocs.io
Python library for spatial single-cell analysis.
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Cancer Cell Line Encyclopedia sites.broadinstitute.org
Database of ~1000 cancer cell lines.
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SIGNOR 2.0 signor.uniroma2.it
Database of causal signaling interactions and pathways, with signed and directed relationships between proteins.
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SIDER (Side Effect Resource) sideeffects.embl.de
Database of 1,430 approved drugs with their recorded adverse drug reactions across 27 system-organ classes.
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SeqBench seqbench.com
Web-based molecular biology sequence workbench for primer design, cloning simulation (Gibson, Golden Gate, restriction digest), CRISPR guide RNA design, and sequence analysis, with a public REST API, OpenAPI 3.1 spec, and MCP server.
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Scanpy scanpy.readthedocs.io
Python library for scRNA-seq analysis.
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Rhea rhea-db.org
Database of chemical reactions.
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Rfam rfam.org
Database of RNA families with sequence alignments and consensus structures.
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Ensembl REST API rest.ensembl.org
API for genomic annotations, variants, genes, and comparative genomics.
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RegNetwork regnetworkweb.org
Database of gene regulatory networks covering transcription factor–target gene and miRNA–gene interaction data across multiple species.
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Reactome reactome.org
Expert-curated, peer-reviewed pathway database with detailed reaction mechanisms.
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PubChem pubchem.ncbi.nlm.nih.gov
One of the largest chemical databases (compounds, genes, and proteins).
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THE HUMAN PROTEIN ATLAS proteinatlas.org
Comprehensive human protein database (cells, tissues, organs).
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