Foundational Tools & Resources

Below is a curated list of the tools, software, and databases that constitute the backbone of modern biological research.

1. The "Must Haves" (Lab Management & 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 & Safety. - Bookmark the safety data sheets (SDS). Boring, but legally required.

2. Data Science & 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 & 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 & 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 & Geospatial

  • QGIS: Free, open-source GIS. - Just as capable as ArcGIS, but free. A must-learn for any field biologist.
  • 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 very easy to misuse statistically. Read the manual carefully.

7. Molecular Biology & 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 & 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 & Visualization (Non-Data)

  • Inkscape: Vector graphics editor. - The free, open-source alternative to Adobe Illustrator. Incredibly powerful.
  • GIMP: Raster image editor. - Free Photoshop. Capable tool, but has a definite learning curve.
  • 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 & 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 & Grad School Survival