Software
MDOP-Labs toolkit
Software
Software is organized into three working tracks aligned with the laboratory's projects, theses, publications, and congress presentations: reproducible development, cancer omics, and protein-structure modeling for molecular dynamics and oncology progression.
Includes curated starting points such as MitoMatch, Tabula Sapiens 2.0, TISCH2, OMIM, AlphaMissense, and complementary tools for building reproducible workflows.
Area
Summary
Showing 32 tools across 3 tracks. Each card includes a purpose, a first action, tags, and a direct source link.
Showing 10 tools · Area: Software Development.
Track 1
Software Development
Build reproducible lab tools, web apps, notebooks, and pipelines.
This track supports the laboratory's software-oriented theses and presentations: Membrane Carromata, automated annotation systems, Snakemake workflows, pathology-AI pipelines, and reusable analysis apps.
Git and GitHub
Version control and collaborative development for code, notebooks, websites, and reproducible analyses.
- Start with
- Create one repository per tool, use issues for research tasks, and keep README-driven examples for students.
- Tags
GitHub Actions
Continuous integration for testing, linting, data checks, and automatic site or documentation builds.
- Start with
- Add a minimal workflow that validates YAML, runs unit tests, and builds documentation on every pull request.
- Tags
Python
Core language for data science, automation, bioinformatics, machine learning, and structural analysis scripts.
- Start with
- Standardize project templates with src/, notebooks/, tests/, environment files, and command-line entry points.
- Tags
R and Bioconductor
Statistical computing and genomics workflows for differential expression, annotation, enrichment, and visualization.
- Start with
- Use R projects with renv or conda environments for reproducible omics analyses and report generation.
- Tags
JupyterLab
Interactive notebooks for exploratory analysis, training, and transparent computational reports.
- Start with
- Pair each notebook with a small test dataset and an exported HTML report for review.
- Tags
Streamlit
Rapid Python web apps for interactive dashboards, screening reports, and student-facing data tools.
- Start with
- Convert stable notebooks into small apps with file upload, cached preprocessing, and downloadable results.
- Tags
Conda / Miniforge
Cross-platform package and environment management for Python, R, bioinformatics, and molecular modeling tools.
- Start with
- Maintain one environment.yml per project and export exact versions for thesis and publication reproducibility.
- Tags
Docker
Containerize software, services, and analysis pipelines so they run consistently across laptops, servers, and cloud/HPC nodes.
- Start with
- Add a Dockerfile for mature tools and document one command that reproduces the main analysis or app.
- Tags
Snakemake
Pythonic workflow system for scalable and reproducible data analyses.
- Start with
- Use it for lab-scale workflows that start as scripts or notebooks and need traceable file-based execution.
- Tags
Nextflow and nf-core
Portable, container-ready workflows for multi-sample omics pipelines across local, HPC, and cloud environments.
- Start with
- Start with nf-core/rnaseq or nf-core/sarek, then wrap lab-specific postprocessing as versioned modules.
- Tags
Track 2
Omics
Explore cancer genomics, single-cell/spatial biology, mitochondrial systems, and variant interpretation.
This track reflects the laboratory's work on gastric, breast, prostate, melanoma, ovarian, colon, and hematological cancers; tumor microenvironment analysis; population-aware precision oncology; and environmental exposure signatures.
MitoMatch
Resource for functionalizing the mitochondrial proteome through predicted human mitochondrial protein-protein interactions.
- Start with
- Use it to nominate mitochondrial interaction hypotheses for transporter, macrophage-metabolism, and cancer-metabolic-reprogramming projects.
- Tags
Tabula Sapiens 2.0
Human single-cell reference atlas for normal tissues, useful as a baseline for disease and tumor-microenvironment comparisons.
- Start with
- Compare candidate genes or cell states from cancer datasets against normal tissue expression patterns.
- Tags
TISCH2
Tumor Immune Single-cell Hub for exploring tumor microenvironment expression across cancer scRNA-seq datasets.
- Start with
- Query macrophage, myeloid, transporter, and immune-state markers before building Scanpy or Seurat analyses.
- Tags
NCI Genomic Data Commons
Repository and computational platform for cancer genomic and clinical data, including TCGA-derived analyses.
- Start with
- Pull harmonized cohorts for gastric, breast, prostate, ovarian, colon, and leukemia analyses before local modeling.
- Tags
NCBI Gene Expression Omnibus
Public repository for high-throughput gene-expression and functional-genomics datasets.
- Start with
- Mine exposure, cancer-cell-line, and validation cohorts for meta-analysis and reproducible reanalysis.
- Tags
Scanpy
Scalable Python toolkit for preprocessing, clustering, visualization, trajectory analysis, and differential expression in single-cell data.
- Start with
- Build a notebook template for TISCH2 or GEO scRNA-seq datasets using AnnData, QC plots, UMAPs, and marker scoring.
- Tags
Seurat
R toolkit for QC, integration, analysis, and exploration of single-cell and multimodal data.
- Start with
- Use it as the R reference workflow for students comparing cell states, datasets, and spatial/transcriptomic modalities.
- Tags
cBioPortal
Interactive exploration, visualization, and download of large-scale cancer genomics datasets.
- Start with
- Use it to rapidly inspect alterations, clinical associations, and cohort-level evidence before scripted analyses.
- Tags
Open Targets Platform
Evidence integration for systematic drug-target identification and prioritization.
- Start with
- Connect candidate genes from omics or structure projects to disease evidence, drugs, variants, and target-disease scores.
- Tags
OMIM
Curated compendium of human genes and genetic phenotypes for rare-disease and hereditary-cancer context.
- Start with
- Use it to contextualize ACVR1, GLUT1/SLC2A1, TMC1, hereditary cancer genes, and genotype-phenotype hypotheses.
- Tags
AlphaMissense
AI-based missense-variant effect predictions for prioritizing protein-changing variants.
- Start with
- Treat scores as research prioritization evidence, not clinical classification, and combine them with ClinVar, population frequency, and structural modeling.
- Tags
nf-core/rnaseq and nf-core/sarek
Community-curated Nextflow pipelines for RNA-seq and DNA-seq/germline-somatic variant workflows.
- Start with
- Use standardized runs for AML transcriptomes, hereditary breast cancer panels, and reproducible NGS processing.
- Tags
Track 3
Protein Structure
Model proteins, mutations, complexes, ligands, membranes, and molecular dynamics mechanisms.
This track supports the laboratory's structural work on GLUT transporters, ACVR1/TGF-β/BMP receptors, telomerase, MYC/NSD3S, peptide design, and pH-responsive or metabolism-linked drug discovery.
RCSB Protein Data Bank
Curated experimental 3D structures for proteins, nucleic acids, ligands, and assemblies.
- Start with
- Begin each structural project by collecting experimental templates, ligands, biological assemblies, and validation metadata.
- Tags
AlphaFold Protein Structure Database
Large-scale access to predicted protein structures for human proteins and other organisms.
- Start with
- Use predicted models when experimental structures are absent, then inspect confidence and domain boundaries before docking or simulation.
- Tags
Boltz-2
Open biomolecular interaction model for predicting complex structures and binding affinities.
- Start with
- Prioritize protein-ligand or protein-complex hypotheses before expensive docking, molecular dynamics, or experimental validation.
- Tags
CHARMM-GUI
Web platform for building reproducible biomolecular simulation systems, including membranes and protein assemblies.
- Start with
- Generate membrane transporter systems for GLUT1, GLUT5, XylE, and hCAT-1 simulations with standardized inputs.
- Tags
OpenMM
High-performance molecular simulation toolkit with Python bindings and GPU acceleration.
- Start with
- Use it for teachable, scriptable simulations and custom analysis workflows linked to notebooks and GPU resources.
- Tags
GROMACS
Molecular dynamics engine widely used for biomolecules, membranes, and coarse-grained/atomistic simulation workflows.
- Start with
- Use it for production simulations where established force-field workflows, performance, and trajectory tools are needed.
- Tags
AutoDock Vina
Open-source docking engine for protein-ligand docking and virtual screening.
- Start with
- Benchmark each target with known ligands or controls before screening candidate inhibitors or modulators.
- Tags
RDKit
Open-source cheminformatics toolkit for molecular formats, descriptors, fingerprints, filtering, and library preparation.
- Start with
- Prepare ligand libraries, remove duplicates, compute descriptors, and connect screening outputs to machine-learning models.
- Tags
PLIP
Protein-ligand interaction profiling for hydrogen bonds, hydrophobic contacts, salt bridges, and related contacts.
- Start with
- Profile docked or simulated complexes to compare interaction persistence across mutations, pH states, or ligands.
- Tags
UCSF ChimeraX
Molecular visualization and analysis for structures, maps, models, and publication-quality figures.
- Start with
- Use it for structure inspection, figure generation, and teaching structural hypotheses before simulation setup.
- Tags
How to begin
Start with Git/GitHub, Conda or Docker, and a small notebook or command-line workflow before scaling to Snakemake, Nextflow, or a Streamlit app.
Use TISCH2, Tabula Sapiens 2.0, GDC, GEO, cBioPortal, OMIM, Open Targets, MitoMatch, and AlphaMissense to define genes, cohorts, cell states, and variants before local analysis.
Move from RCSB or AlphaFold models to Boltz-2, docking, membrane-system setup, molecular dynamics, and interaction profiling when a mechanistic structural question is justified.