Research projects you can open in a browser
The tools section holds single-purpose utilities that run one command each. This page lists the larger builds: complete pipelines that take an input dataset through several analytical stages and hand back results and a report. Each one covers a task that normally needs a cluster, a container and a working environment, which is exactly what makes them awkward to reproduce on a laptop or in a teaching lab.
They are built the same way: the analysis runs client-side in your browser tab, so your data is processed on your own device rather than uploaded somewhere. Each project page documents the method, the parameters it uses and the limits of what it can tell you, so you can judge whether it is the right tool before you trust the output.
Which project do you need?
Match the question you are trying to answer to the pipeline that answers it:
- Which genes change between conditions? Use RNA-seq Analysis Tool for raw reads through FastQC, trimming, alignment, quantification and DESeq2, with WGCNA for co-expression modules.
- Do genotype, expression and copy number agree? Use Multi-Omics Integration Tool to bring the three layers together and test association with MFA or iCluster.
- How do genomes differ across species or samples? Use Comparative Genome Analysis to compare up to 10 FASTA genomes with annotation and SNP review.
- Where does a binding or accessibility peak sit? Use Cancer Genomics NGS Pipeline for ChIP-seq and ATAC-seq quality control, alignment and peak calling.
- Will this ligand bind, and in what pose? Use DockTool for multi-seed docking with 3D inspection and a downloadable report.
- Is the structure stable over time? Use MD Simulation Workflow Builder for the GROMACS sequence from topology through NVT/NPT equilibration to production MD.
- What drives activity across a compound series? Use QSAR Modelling Tool to fit regression models on ligand data and explore molecular descriptors.
What every project here has in common
Standard, published methods
The pipelines wrap established software and algorithms — DESeq2, edgeR-style quantification, MFA, iCluster, AutoDock-style search, GROMACS — so the results are comparable with what a local install produces.
Runs on your device
Analysis happens in browser memory, so files are not transmitted to a third-party server. The privacy policy sets out exactly what is and is not collected.
Every stage is a step you can see
Parameters and thresholds are editable rather than buried, so a surprising result can be traced to the step that produced it instead of being taken on trust.
Honest about the limits
These are working pipelines for research, teaching and prototyping. They are not validated clinical software, and each project page says where the method stops being reliable.
Access
Most projects need a free account so your results stay attached to you. Marked sign-in required below means the project opens after you log in; the QSAR Modelling Tool opens straight away. Processing itself still happens in your browser either way.
Comparative Genome Analysis
Compare up to 10 FASTA genomes side by side: annotation, SNP and mutation review, and transcription-factor analysis.
Cancer Genomics NGS Pipeline
NGS ChIP-seq and ATAC-seq pipeline for cancer genomics: quality control, alignment, peak calling and reporting.
RNA-seq Analysis Tool
Raw reads to differential expression: FastQC, trimming, Rsubread alignment, featureCounts, DESeq2 and WGCNA.
Multi-Omics Integration Tool
Integrate gene expression, mutation and copy-number data in one workspace, with MFA and iCluster association.
DockTool Protein-Ligand Docking
Upload receptor and ligand, set the docking box, run multi-seed docking, then analyse poses in 3D and export a report.
MD Simulation Workflow Builder
Step-by-step GROMACS MD workflow: topology, solvation, ions, minimisation, NVT/NPT, production run and analysis.
QSAR Modelling Tool
QSAR analysis on ligand activity data with OLS regression, molecular descriptors, interactive charts and report export.
Frequently asked questions
Do I need to install anything to use these projects?
No. Each project runs in the browser and is served from this site, so there is no package to install, no environment to activate and no cluster to queue on. Open a project, load your data and run the analysis. That also makes the projects usable on a locked-down bench machine or a borrowed laptop.
Do the projects upload my data to a server?
The projects run client-side in your browser tab, so files are read into browser memory and processed on your own device rather than being transmitted. Nothing about your inputs is sent to a third-party analysis service. The privacy policy sets out exactly what is and is not collected.
Why do most of these projects ask me to sign in?
Six of the seven workspaces are gated behind an account so that uploaded data, saved results and reports stay tied to the person who created them. The QSAR Modelling Tool is the exception and opens without signing in. Sign-in only controls access to the workspace; it does not move your compute off your machine.
How are these different from the tools section?
The tools section holds single-purpose utilities that run one command each, such as a SAM/BAM viewer or a BED interval calculator. The projects here are complete multi-step workflows: RNA-seq from raw reads to differential expression, multi-omics integration, a GROMACS MD protocol, a docking campaign. They call several methods in sequence and produce a report at the end.
Can I use the results in a paper or a thesis?
Yes, but check them first. These projects implement standard published methods and are built for analysis, teaching and prototyping rather than as validated clinical software, so verify the output independently before relying on it in a formal or clinical context.
How big a dataset can these handle?
It depends on your device memory, because inputs are loaded into the browser. Small to medium datasets work well, which suits method development and teaching. For large cohorts or production batch runs, install the same underlying software locally and keep the scripts as the record of what was run.
Can I use a project on confidential or unpublished data?
From a privacy standpoint, yes. Because the compute happens on your device, embargoed sequencing data, patient-derived results and pre-submission analyses can be worked on without transferring the files elsewhere. Still follow your institution's own data-handling agreements and access controls.
How do I report a bug or ask for a new analysis?
Use the contact page and describe the step that failed, the input format and the result you expected. If you are working with patient data or anything sensitive, describe the shape of the problem without including the data itself.