KalarisLabs/research-agent-skills

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Drives the Fictiv on-demand manufacturing web app (app.fictiv.com) in the user's browser, since there is no public API. Covers uploading CAD files (STEP, SLDPRT, STL), configuring process, material, finish, threads and tolerances, reading DFM feedback, instant or manual quotes, lead-time tiers, checkout by card or PO…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex needs its repo

Fine-tunes and evaluates OpenVLA-OFT and OpenVLA-OFT+ policies for robot action generation with continuous action heads, LoRA adaptation, and FiLM conditioning on LIBERO simulation and ALOHA real-world setups. Use when reproducing OpenVLA-OFT paper results, training custom VLA action heads (L1 or diffusion), deploying…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex needs its repo

Fine-tune and serve Physical Intelligence OpenPI models (pi0, pi0-fast, pi0.5) using JAX or PyTorch backends for robot policy inference across ALOHA, DROID, and LIBERO environments. Use when adapting pi0 models to custom datasets, converting JAX checkpoints to PyTorch, running policy inference servers, or debugging…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Fine-tune LLMs using reinforcement learning with TRL - SFT for instruction tuning, DPO for preference alignment, PPO/GRPO for reward optimization, and reward model training. Use when need RLHF, align model with preferences, or train from human feedback. Works with HuggingFace Transformers.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Query Firecrawl Research Index paper endpoints for topic discovery, source metadata, question-matched passages, and citation-neighbor expansion. Use when a researcher explicitly asks for Firecrawl Research or its hosted arXiv and biomedical paper records.

KalarisLabs/research-agent-skills

Skill Claude Code

Read, inspect, and write Flow Cytometry Standard (FCS) 2.0, 3.0, and 3.1 files with FlowIO. Use for low-level FCS metadata and channel inspection, NumPy event extraction, multi-dataset files, table export, and FCS 3.1 creation; use FlowKit for compensation, cytometry transforms, gating, or FlowJo workspaces.

KalarisLabs/research-agent-skills

Skill Claude Code

Plan, configure, inspect, restart, and analyze bounded FluidSim computational-fluid-dynamics simulations with explicit numerical-validity and HPC safety checks. Use for FluidSim solver selection, parameter review, FFT/MPI setup, output diagnostics, or restart compatibility.

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Retrieve ClinGen gene-disease validity assertions for a public gene or disease, and review source-linked public evidence and literature for one supported GRCh38 germline nuclear SNV or simple indel through Folklore Clinical Variant Interpretation MCP. Use when a scientific agent must branch deterministically on…

KalarisLabs/research-agent-skills

Skill Claude Code

Generate or edit images with AI models through the OpenRouter Image API (Gemini, Seedream, Recraft, GPT-Image, Riverflow). Use for photos, illustrations, artwork, concept art, visual assets, logos, and image editing or compositing from reference images. For flowcharts, circuits, pathways, and other technical diagrams…

KalarisLabs/research-agent-skills

Skill Claude Code

Plans and audits local genomic-interval machine learning workflows with Geniml (0.8.4) and Gtars: validates BED files against chromosome sizes and assembly contracts, plans Region2Vec, scEmbed, and BEDspace runs, checks model, tokenizer, and universe.bed compatibility, and assesses consensus universes (CC, CCF, ML…

KalarisLabs/research-agent-skills

Skill Claude Code

Convert genomic intervals between coordinate conventions, normalise and compare variant representations, and detect assembly or contig-naming mismatches before they corrupt an analysis. Use whenever coordinates cross a format, tool, or assembly boundary - converting between BED, GFF/GTF, VCF, SAM/BAM, WIG, PSL…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Predict regulatory features, gene structure, and expression directly from DNA sequence using Genomic Intelligence's hosted transformer DNA language models — no local GPU or model weights. Six tasks over a REST API and a hosted MCP server (keyless public demo): promoter regions, splice donor/acceptor sites, enhancer…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Provides geospatial and Earth observation workflows using GeoPandas, Rasterio, GDAL, Xarray, Shapely, Laspy, PDAL, Google Earth Engine, and STAC/Planetary Computer, covering Sentinel, Landsat, MODIS, SAR and hyperspectral imagery, spectral indices, terrain and network analysis, point clouds, COGs, CRS handling, and…

KalarisLabs/research-agent-skills

Skill Claude Code

Guidance and local audit CLIs for Python workflows using GeoPandas 1.1.4 GeoSeries and GeoDataFrame for planar vector data: CRS handling, geometry validity and repair, sjoin, overlay, clip, dissolve, union, GeoPackage, GeoParquet and PostGIS I/O, and plotting. Use when reprojecting or assigning a CRS, auditing invalid…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Detect host inventory and effective CPU, memory, disk, scheduler, container, and accelerator limits when a user asks for resource-aware planning or before a clearly resource-sensitive local workload. Produces a redacted JSON snapshot and conservative planning helpers without stress tests or assuming visible host…

KalarisLabs/research-agent-skills

Skill Claude Code

Queries 20+ bioinformatics databases and analysis services through the gget CLI and Python package, covering Ensembl gene search, info and sequences (ref, search, info, seq), BLAST, BLAT, MUSCLE, DIAMOND, PDB, AlphaFold, ELM, ARCHS4, CELLxGENE, Enrichr, Bgee, OpenTargets, cBioPortal, COSMIC, viral sequence downloads…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

GGUF format and llama.cpp quantization for efficient CPU/GPU inference. Use when deploying models on consumer hardware, Apple Silicon, or when needing flexible quantization from 2-8 bit without GPU requirements.

KalarisLabs/research-agent-skills

Skill Claude Code

Submit and manage protocols on Ginkgo Bioworks Cloud Lab (cloud.ginkgo.bio), a web-based interface for autonomous lab execution on Reconfigurable Automation Carts (RACs). Use when the user wants to run protein expression and purification (cell-free, E. coli, or Pichia), HiBiT or A280 or LabChip quantification, IVT…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Quantizes LLMs to 4-bit (also 3-bit) with GPTQ using group-wise quantization (group size 128 by default), via AutoGPTQ and transformers. Covers loading pre-quantized GPTQ models, quantizing your own model, choosing group size, selecting ExLlamaV2, Marlin, or Triton kernels, and QLoRA fine-tuning with PEFT. Use when…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Guides GRPO (Group Relative Policy Optimization) fine-tuning of language models with the TRL library, including GRPOTrainer configuration, composing multiple reward functions (correctness, format, length, style), dataset prep in chat format, Unsloth setup, LoRA merging, and monitoring reward, rewardstd and KL. Use…

KalarisLabs/research-agent-skills

Skill Claude Code

Inspects and plans work with Gtars, the Rust/Python/CLI toolkit for genomic intervals: BED RegionSet set algebra (reduce, setdiff, intersect, closest, cluster, gaps), overlap counts, consensus peak sets, coverage, tokenizers, fragment processing, and refget/BEDbase stores. Use when merging or comparing BED interval…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Constrains LLM output during generation with Guidance (Microsoft Research), using regex, select() choices, context-free grammars, token healing, and @guidance functions, with Anthropic, OpenAI, Transformers, and llama.cpp backends. Use when you need generated text to match a regex or fixed format such as dates…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Extracts tiles and preprocesses H&E whole slide images with the histolab Python library (OpenSlide), covering slide inspection, tissue masks (TissueMask, BiggestTissueBoxMask), RandomTiler, GridTiler and ScoreTiler extraction, image and morphological filters, and Macenko or Reinhard stain normalization. Use when…

KalarisLabs/research-agent-skills

Skill Claude CodeCodex

Half-Quadratic Quantization for LLMs without calibration data. Use when quantizing models to 4/3/2-bit precision without needing calibration datasets, for fast quantization workflows, or when deploying with vLLM or HuggingFace Transformers.