12,426 tagged Scientific, measured the same way as everything else here.
Browse within: bioinformatics 260ai-scientist 207LLM 186agents 186biology 170reasoning-language-models 165ai-scientists 164reasoning-agent 164tool-use 164agent 159data-analysis 133cancer-genomics 132computational-biology 132literature-review 120
learningmatter-mit/AtomisticSkills
Skill Claude CodeCodex
Compute single-trajectory MM-GBSA and / or MM-PBSA binding free energy estimates from a protein-ligand MD trajectory. Two backends: a fast OpenMM GBn2 path (no extra dependencies) and an AmberTools MMPBSA.py path that supports both GB (multiple igb models) and Poisson-Boltzmann PB on the same trajectory.
Skill Claude CodeCodex
Complete workflow for single-cell RNA-seq analysis using Seurat v5. Process raw data through quality control, normalization, clustering, and cell type annotation with publication-ready visualizations.
Skill Claude CodeCodex
Workflow 3: Full paper writing pipeline. Orchestrates paper-plan → paper-figure → paper-write Markdown drafts → paper-write LaTeX section files → paper-compile → paper-review → formal polish → optional human-style polish → proof/claim/citation audits to go from a narrative report to a polished PDF. Use for /goal-based…
Skill Claude Code ✓ vendor
How to run domain-decomposed (multi-GPU) MLIP simulations with DomainParallel — choose between the halo and graph-partition strategies, author a distributionspec so a bring-your-own model runs under domain decomposition, and write a custom dynamics integrator that stays correct across ranks.
adaptyvbio/protein-design-skills
Skill Claude CodeCodex
Quality control metrics and filtering thresholds for protein design. Use this skill when: (1) Evaluating design quality for binding, expression, or structure, (2) Setting filtering thresholds for pLDDT, ipTM, PAE, (3) Checking sequence liabilities (cysteines, deamidation, polybasic clusters), (4) Creating multi-stage…
Skill Claude CodeCodex
Run QC scripts on a VDJdb chunk, report every error with a suggested fix, verify the output of previous /extract and /format steps, estimate confidence scores, and flag gaps in current pysrc QC coverage.
Skill Codex
Search arXiv and, when needed, verify external academic sources to update field beliefs and one primary decision through testable propositions, capability frontiers, explicitly labeled mechanism models, technical options, transition theses, five-dimensional maturity, leading indicators, and a restrained bilingual…
Skill Claude CodeCodex
Run OmniScientist end to end in the OmniScientist CLI using DeepSeek V4 Flash. Turn raw research data (images, signals, audio, video, 3-D, tables, or graphs) and an open direction into perceived evidence, a falsifiable hypothesis, recorded analysis, real citations, a gated candidate paper, PDF, and Overleaf bundle.…
Skill Claude CodeCodex
Extracts process simulation data from unstructured sources (text, tables, PFDs, data sheets, STID/E3D line lists) and converts it to NeqSim JSON builder format or PipingRouteBuilder route models. USE WHEN: a user provides a process description, PFD, operating data, line-list table, or design document and wants a…
Skill Claude CodeCodex
Default path for any cloud training work in Dat. Use this skill whenever a task needs cloud training, GPU training, model fine-tuning, training evaluation, long-running training compute, or hosted training job orchestration. Also use it to submit prepared packages, handle approval/session handoff, track jobs, cancel…
Skill Claude CodeCodex
Query visual scientific figure references, show candidates for human preference selection, export selected reference bundles, and guide plotting agents from human-selected visual examples to code action.
alfredolopez80/multi-agent-ralph-loop
Skill Claude Code
Autonomous experiment loop: modifies code, runs experiments, evaluates metrics, keeps improvements. Inspired by karpathy/autoresearch + pi-autoresearch + autoexp. Triggers: /autoresearch, 'auto research', 'optimize continuously', 'experiment loop', 'autonomous optimization'.
Skill Claude CodeCodex
A skill for Bazi, also called Four Pillars, a traditional system that uses birth details to calculate charts, cycles, and relationships between chart elements.
Skill Claude CodeCodex
Analyze Simulink Profiler results to find simulation bottlenecks or compare two profiler sessions to identify regressions. Use when asked to profile a Simulink model, analyze profiler data, find what is slow, or compare simulation performance between two runs or releases.
Skill Codex
Reference-aware whole-paper reading and structured research-note generation. Use when the user wants to understand an entire paper, place it in the literature, compare it against core prior work or baselines, or decide whether a paper should be read as a method paper or as a Nature or Science-style evidence-chain…
Skill Claude CodeCodex
Turn math and physics concepts into rendered Manim films.
limi124/remote-sensing-research-radar
Skill Codex
Track, retrieve, screen, and synthesize research frontiers for geospatial AI, remote sensing big data, and transferable computer vision methods. Use when Codex is asked to search recent papers, arXiv, GitHub projects, Papers with Code, datasets, benchmarks, competitions, or conference/workshop programs in remote…
Skill Claude CodeCodex
A Chinese-language reference skill for traditional Chinese medicine, including its theories, diagnostic approaches, herbs, formulas, and treatment principles.
Skill Claude CodeCodex
Use when inspecting YAM logs, videos, SAM3 overlays, observations, planner previews, function-call JSON, result files, or failure evidence.
Skill Claude CodeCodex
Evidence-based endurance coaching protocol (v11.63). Use when analyzing training data, reviewing sessions, generating pre/post-workout reports, planning workouts, answering training questions, or giving endurance coaching advice. Always read or fetch athlete JSON data before responding to any training question.
jinzhezenggroup/computational-chemistry-agent-skills
Skill Claude CodeCodex
Fine-tune a DPA3 model in DeePMD-kit using the PyTorch backend. Use when the user wants to adapt a pre-trained DPA3 model to a new downstream dataset. Supports fine-tuning from a self-trained DPA3 model (.pt checkpoint), from a multi-task pre-trained model, or from a built-in pretrained model downloaded via dp…
Skill Claude CodeCodex
A skill for turning research papers and other scientific material into reusable prompts for AI-generated figures. It can also use reference images when available.
Skill Claude CodeCodex
Invoke this skill when an OCI diagnostic fails or warns and a spec change is needed. Keywords: covariate balance failure, overlap warning, placebo warning ATOTHRESHOLD, trimming extreme propensities changing estimand: ATE → ATT, ATE → ATO adding covariates, dataset insufficiency actor-critic feedback loop, suggested…
Skill Claude Code
Use when bringing a URDF robot, hand, or CAD-generated model into MuJoCo MJCF and no hand-tuned upstream MJCF exists.
At most 3 mods per repository are shown here, and a mod shipped inside a plugin is left to that plugin's page — the rest are on their repository pages: