SciTools

Useful tools and resources for your scientific research.

Literature and note-taking

• Zotero. Reference manager. Get all your papers in one place
• Inciteful. Paste a DOI and find related papers, using cross citations
• Research Rabbit. Upload a BibTeX or connect to your Zotero account, and find papers related to your collection
• Obsidian. Note-taking app in markdown format, with cross-references. (Note that this page was created with Obsidian!)

Documents and graphs

• WebPlotDigitizer. Extract numerical data from plotted images
• Pix2Tex. Write LaTeX equations by uploading a screenshot
• Detextify. Find that weird LaTeX symbol
• Tables Generator. Create tables in different formats: LaTeX, markdown…
• Draw.io. Create nice diagrams and flowcharts
• TeX Live + VSCode with LaTeX Workshop extension, for local LaTeX edition. Install on Linux as sudo apt install texlive-full

File managing tools

• Git. Please use a version tracker for your code. Please.
• FreeFileSync. Sync backups of entire folders with the click of a button
• TorrentTrackers. Selection of nice torrent trackers, to share big files such as large computational outputs

Chemistry tools

• PTable. Periodic Table
• IUPAC Periodic Table of the Elements and Isotopes
• ACS Solvent selection tool

Solid-state physics software

• QuantumESPRESSO (DFT)
• CASTEP (DFT)
• McStas Monte Carlo simulations of neutron instrumentation
• ASE Atomic Simulation Environment for Python
• cif2cell tool for structural file conversion
• StructuralDB. Comprehensive list of relevant material databases, useful to find structural files to simulate your materials
• ATON. Python package for easy text-edition tasks and custom APIs, such as Quantum ESPRESSO or SLURM
• Wikipedia’s DFT software comparison: List of quantum chemistry and solid-state physics software
• Wikipedia’s Molecular Dynamics software comparison: Comparison of software for molecular mechanics modeling
• CrysAlisPro For XRD measurements

Scientific illustrations

• Inkscape for vector graphics and posters, check Inkscape tutorials
• Blender for 3D modelling, check Blender tutorials
• FreeCAD Free and Open Source CAD for 3D parametric modeling
• NIH Bioart CC license
• Chemix !!! Attribution required unless subscribed
• BioRender !!! Subscription required for publishing
• SciDraw !!! CC-BY
• Bioicons !!! Check licensing

LLM tools

Warning: Writing is thinking. If you don’t write, you are not thinking doi.org/10.1038/s44222-025-00323-4. AI should not replace your own intelligence. It may be useful e.g. for debugging code, but you must be the one designing the code, otherwise it will create stupid routines that lead nowhere, etc. It is not creative by itself, that’s on you. On top of that, running local models is a must if you don’t want to fuel the machine while giving away your private data for free. And be careful not to develop a dependency from these tools. Mind that stochastic parrots raise important social and environmental challenges, and you should use them with care, see doi.org/10.1145/3442188.3445922 or doi.org/10.2139/ssrn.4678265.

Local

• Ollama. Run local LLM models
• Meetily. Meeting assistant

Online (a.k.a. giving away for free your personal data and your soul)

• HuggingChat. Open source LLMs
• GitHub Copilot. VSCode plugin that helps you write code, free with the university account. It also adds a chat window to get coding insights
• Elicit. Ask a Question, get summarized results from papers
• Deepl Write. Check your grammar or translate, really useful even for scientific texts
• Microsoft Copilot
• Google Gemini
• ChatGPT
• DeepSeek

Other GitHub repositories

• SciTools. Links, tutorials and resources for all your scientific endeavours (this page)
• PlantillaLatex. LaTeX template, with info and description of useful commands

Contact

Pablo Gila-Herranz, pgila001@ikasle.ehu.eus
PhD Student @ Quantum Beams & Computation for Sustainable Materials Group
Materials Physics Center (CFM-MPC), CSIC-UPV/EHU

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Last updated on 2025-10-21