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Foundational tools and resources.

A curated list of the tools, software, and databases that constitute the backbone of modern biological research. Grouped by area, with short mentor notes about when and why to reach for each one.

1. The must-haves: lab management and protocols

Protocols.io The open-access standard for sharing detailed methods. Essential for reproducibility; don't just keep it in a paper notebook.

Quartzy Lab supply management and ordering. Great for keeping the lab manager (and the budget) sane.

OpenWetWare Wiki-based lab protocols. A bit old-school, but still a goldmine for classic molecular recipes.

Addgene Non-profit plasmid repository. If you need a construct, look here before you try to build it yourself.

TAMU EHS Environmental Health and Safety. Bookmark the safety data sheets (SDS). Boring, but legally required.

2. Data science and coding, the backbone

R Project The statistical lingua franca of biology. You cannot avoid this. Learn it early.

RStudio (Posit) The essential IDE for R. Do not try to use the base R GUI; this is the industry standard.

Python The glue of bioinformatics. Better than R for heavy text processing and building complex pipelines.

Anaconda/Conda Package manager for Python/R. Saves you from "dependency hell" when installing software.

Jupyter Notebooks Interactive computing. Great for teaching and sharing analyses, less great for production pipelines.

Git & GitHub Version control and hosting. Steep learning curve, but saves you when you delete your thesis analysis by accident. If it's not on GitHub, did you even write it?

Stack Overflow The oracle. Copy-pasting from here is 50% of a bioinformatician's job.

Regex101 Regular expression tester. A life-saver for cleaning messy data files.

TAMU HPRC Texas A&M High Performance Research Computing. When your laptop creates smoke, move your job here. Excellent support team.

3. Statistics and reproducibility

G*Power Statistical power analysis. Use this before you start your experiment, not after you realize your p-value is 0.06.

OSF (Open Science Framework) Project management for open science. The best place to pre-register your studies.

Dryad & Zenodo Data repositories. The standard for ecology/evolution papers. Zenodo gives you a DOI for code or posters.

4. Genomics, the heavy lifters

Bioconductor The R repository for genomic data. Essential, but updates can sometimes break your old scripts.

Samtools The swiss-army knife for DNA sequencing data. Fast, command-line based, and absolutely essential.

BEDTools "Genome arithmetic." For when you need to know what overlaps with what.

FastQC & Trimmomatic Quality control and cleaning. The first things you run on any new dataset.

IGV (Integrative Genomics Viewer) Visualizing genome alignments. The best way to "see" your mutations and verify your code isn't lying to you.

5. Phylogenetics: inference and visualization

IQ-TREE Modern maximum likelihood. Currently the best balance of speed and accuracy for most users.

RAxML-NG The successor to the classic RAxML. Great for massive datasets.

MrBayes / RevBayes Bayesian inference. MrBayes is the classic; RevBayes is powerful but has a steep learning curve.

FigTree The classic tree viewer. Simple and effective, though showing its age.

iTOL (Interactive Tree of Life) Web-based tree annotator. Makes beautiful publication-quality figures, but it is online-only.

ggtree R package for trees. Hard to learn, but allows for fully programmable and reproducible tree graphics.

6. Ecology, fieldwork, and geospatial

QGIS Free, open-source GIS. As capable as ArcGIS, and free. The standard for field biologists.

iNaturalist Citizen science data. A massive database of species occurrences and a great way to verify ID.

GBIF Global Biodiversity Information Facility. The raw data hose for biogeography.

WorldClim Global climate data. The standard input for niche modeling.

Maxent Species distribution modeling. User-friendly, but easy to misuse statistically. Read the manual carefully.

7. Molecular biology and general tools

SnapGene Viewer Plasmid mapping. The industry standard viewer is free and excellent.

ApE (A Plasmid Editor) Free cloning tool. Ugly interface, but rock-solid logic for planning constructs.

Primer3 PCR primer design. The engine behind almost every primer tool on the web.

ImageJ / Fiji Scientific image analysis. Java-based and clunky, but the absolute king of microscopy analysis.

UniProt & PDB Protein databases. The gold standards for protein annotation and 3D structure.

8. Writing, citing, and publishing

Overleaf Online LaTeX editor. The best way to write collaborative papers without formatting headaches.

Zotero Reference manager. Free, open-source, and arguably better than EndNote. Use the browser connector!

Sherpa Romeo Copyright policies. Checks if you are legally allowed to post your PDF on your website.

ORCID Digital ID. Get one. Now. It follows you forever.

BioRxiv The biology preprint server. Post your paper here before you submit to a journal to get early feedback.

TAMU Writing Center University resource. They have specific consultants for scientific writing and dissertation formatting.

9. Graphics and visualization (non-data)

Inkscape Vector graphics editor. The free, open-source alternative to Adobe Illustrator. Works at publication scale.

GIMP Raster image editor. Free Photoshop. Capable, but steep to learn.

ColorBrewer Color advice. Stop using default red/green color scales. Use this to make accessible maps.

BioRender Scientific illustration. Makes professional diagrams easy, but be aware everyone's figures are starting to look the same.

10. Career, culture, and sanity

Academic Tree Genealogy of science. Find out who your academic "grandparents" are. Fun for seeing lineage.

PhD Comics The documentary of our lives. It stops being funny and starts being painful around year 4.

XKCD Nerdy humor. There is a relevant comic for everything in science.

ResearchGate Social network for scientists. Spams your email, but actually useful for asking authors for PDFs.

11. Mentoring and grad school survival

The Professor Is In Career advice. Hard truths about the academic job market. Read this early, not right before you graduate.

Science Careers (AAAS) Career resources. Excellent articles on non-academic paths and lab management.

Individual Development Plan (IDP) Career planning tool. A structured way to plan your career goals. Required by many grants, but useful for everyone.

TAMU Grad School Graduate school resources. Know the rules. They control your dates, deadlines, and dissertation formatting.

National Center for Faculty Development & Diversity Professional development. A&M usually has a membership. Great for writing accountability and time management.

Community contribution

This list is living and breathing. If you are a student or faculty member and have a tool that saved your thesis or accelerated your research, please email us. We are especially looking for resources that help early graduate students through the first few years.