Workbench Module LIVE

27 scientific tools across 3 hubs. Computational analysis replacing £250–500K/year in commercial licences. Compute tools by Don Daley.

Tools

Hubs

Containers

Pages

SPR Models

"Never a black box": Every calculation shows its engine, equation, academic reference, and parameter descriptions. Users always know exactly what algorithm produced their result and what assumptions it makes.

URLs

Environment	URL	Status
Production	`https://app.discoverant.com/workbench`	LIVE
Development	`https://dev.discoverant.com/workbench`	LIVE

Architecture

Two-Server Design (Target State)

Component	Dell 1 — Platform (192.168.1.101)	Dell 2 — Compute (192.168.1.102)
Runs	Frontend, Backend, Workbench API, PostgreSQL, Redis, nginx	Don's Docker services (Combi, Kinetics, Molecular)
RAM	~14 GB	~2–8 GB depending on active jobs
Data	All compound data, user accounts, files	None — stateless
If it crashes	Platform unavailable, data safe	Compute offline, platform unaffected

Current state: All services running on Dell 1 (single server). Dell 2 to be configured for compute isolation. One environment variable to switch: COMPUTE_HOST=192.168.1.102

Compute Tiers

Tier	Response	CPU / RAM	UX	Examples
INSTANT	< 1s	Negligible	Synchronous, inline	Property calc, PAINS, Ro5, fingerprints, format conversion
FAST	1–30s	1–2 cores, 500 MB	Spinner	IC50 fitting, Michaelis-Menten, R-group enum, conformers
HEAVY	30s – 10m	2–4 cores, 2 GB	Progress bar + Cancel	Molecular docking, SPR fitting, ADMET, PaDEL descriptors
INTENSIVE	10m – hours	4+ cores, 4–8 GB	Job queue + SSE + Kill	Quantum chemistry (PySCF), batch docking, large library enum

Nginx Proxy Routes

location /workbench-api/combi/     → http://127.0.0.1:8083/   # Combi-Hub
location /workbench-api/kinetics/  → http://127.0.0.1:8091/   # Kinetics-Hub
location /workbench-api/molecular/ → http://127.0.0.1:8090/   # Molecular Gateway

All API calls from frontend go through nginx, never direct port numbers. Timeout: 600s for long-running compute.

Combi-Hub — Library Design

Port 8083 · FastAPI + RDKit · github.com/Donald-Daley/adroit_combi-hub

Commercial equivalent: BIOVIA Library Design (£40–100K/yr), Schrödinger CombiGlide

Endpoint	Method	Description
`/api/enumerate`	POST	R-group enumeration → array of SMILES with properties
`/api/depict`	POST	Batch depiction → single SVG grid
`/api/depict_list`	POST	Individual SVG images
`/api/properties`	POST	Property profiles (MW, logP, TPSA, HBD/HBA, complexity, risks)
`/health`	GET	Health check

Kinetics-Hub — Curve Fitting, SPR & ADMET

Port 8091 (API) · 8081 (SPR UI) · 8082 (ADMET UI) · FastAPI + SciPy + RDKit

Commercial equivalent: GraphPad Prism (£1–5K/seat), Cytiva BIAevaluation (£10–20K/yr), Optibrium StarDrop (£15–30K/yr)

Endpoint	Method	Description
`/fit/ic50`	POST	4PL dose-response → IC50, Hill slope, R², fitted curve
`/fit/mm`	POST	Michaelis-Menten → Km, Vmax, fitted curve
`/fit/scatchard`	POST	Scatchard binding plot
`/fit/rosenthal`	POST	Rosenthal binding plot
`/fit/klotz`	POST	Klotz binding plot
`/fit/spr`	POST	SPR sensorgram fitting → ka, kd, KD, chi², residuals
`/health`	GET	Health check

SPR Models (6)

1:1 Langmuir 1:1 + Mass Transport Heterogeneous Ligand Bivalent Analyte Two-State Conformational Competing Analytes

Molecular-Hub — Computational Chemistry Gateway

Port 8090 (gateway) · 8080 (UI) · 11 microservices · FastAPI + Vina + PySCF + AmberTools + OpenBabel + RDKit + OpenMM + PaDEL + STOUT + OPSIN

Commercial equivalent: Schrödinger Glide/Maestro (£80–300K/yr), Gaussian (£5–30K/seat), Dragon/alvaDesc (£5–15K/yr)

Endpoint	Method	Service	Description
`/convert`	POST	OpenBabel	Format conversion (any → any)
`/charges`	POST	Amber	Partial charge calculation
`/dock`	POST	Vina	Molecular docking (receptor + ligand)
`/conformers`	POST	OpenMM/RDKit	3D conformer generation
`/homo_lumo`	POST	PySCF	Quantum orbital energies
`/fingerprints`	POST	RDKit	Molecular fingerprints
`/rdkit/descriptors`	POST	RDKit	Molecular descriptors from SDF
`/padel`	POST	PaDEL	PaDEL descriptor calculation
`/structure_to_name`	POST	STOUT	SMILES → IUPAC name
`/name_to_structure`	POST	OPSIN	IUPAC name → SMILES
`/props_topology`	POST	RDKit	Topological properties
`/props_substructure`	POST	RDKit	Substructure properties
`/props_shape`	POST	RDKit	Shape properties
`/openbabel/formats`	GET	OpenBabel	List supported formats
`/health`	GET	Gateway	Health check

Frontend Pages

Route	Page	API
`/workbench`	Landing — 8 workflow cards + search	—
`/workbench/ic50`	Dose-response IC50 fitting	`/workbench-api/kinetics/fit/ic50`
`/workbench/kinetics`	Michaelis-Menten + transforms	`/workbench-api/kinetics/fit/mm`
`/workbench/spr`	SPR sensorgram fitting (6 models)	`/workbench-api/kinetics/fit/spr`
`/workbench/library`	R-group enumeration + filtering	`/workbench-api/combi/api/enumerate`
`/workbench/docking`	Molecular docking (Vina)	`/workbench-api/molecular/dock`
`/workbench/conformers`	3D conformer generation	`/workbench-api/molecular/conformers`
`/workbench/quantum`	HOMO/LUMO quantum properties	`/workbench-api/molecular/homo_lumo`
`/workbench/admet`	ADMET prediction dashboard	`/workbench-api/kinetics/`

Method Transparency — Academic References

Every workflow page includes expandable MethodCard components showing engine, model, equation, parameters, and primary academic reference.

Tool	Reference
IC50 (4PL)	Hill, A.V. (1910). J Physiol 40:iv-vii
Michaelis-Menten	Michaelis & Menten (1913). Biochem Z 49:333-369
SPR fitting	Karlsson & Fält (1997). J Immunol Methods 200:121-133
Molecular docking	Trott & Olson (2010). J Comput Chem 31:455-461
Conformers (ETKDGv3)	Riniker & Landrum (2015). J Chem Inf Model 55:2562-2574
Quantum (PySCF)	Sun et al (2018). WIREs Comput Mol Sci 8:e1340
PAINS	Baell & Holloway (2010). J Med Chem 53:2719-2740
BRENK	Brenk et al (2008). ChemMedChem 3:435-444
Ro5	Lipinski et al (1997). Adv Drug Deliv Rev 23:3-25

Container Inventory (15 containers)

Container	Port	Status
`combi_hub`	:8083	RUNNING
`adroit_kinetics-hub-backend-1`	:8091	RUNNING
`adroit_kinetics-hub-spr-frontend-1`	:8081	RUNNING
`adroit_kinetics-hub-admet-frontend-1`	:8082	RUNNING
`molhub-gateway`	:8090	RUNNING
`molhub-frontend`	:8080	RUNNING
`molhub-openbabel`	internal	RUNNING
`molhub-padel`	internal	RUNNING
`molhub-vina`	internal	RUNNING
`molhub-amber`	internal	RUNNING
`molhub-openmm`	internal	RUNNING
`molhub-psi4`	internal	RUNNING
`molhub-rdkit`	internal	RUNNING
`molhub-stout`	internal	RUNNING
`molhub-opsin`	internal	RUNNING

Full Port Map

Port	Service	Notes
3100	discoverant-frontend-prod	Production React
3001	discoverant-frontend-dev	Development React
8000	discoverant-backend-prod	Production FastAPI
8001	discoverant-backend-dev	Development FastAPI
5432	discoverant-postgres	PostgreSQL + Bingo
6379	discoverant-redis	Redis
8080	molhub-frontend	Molecular Hub UI (Don's)
8081	kinetics-spr-frontend	SPR UI (Don's)
8082	kinetics-admet-frontend	ADMET UI (Don's)
8083	combi_hub	Combi-Hub API + UI
8090	molhub-gateway	Molecular Hub API gateway
8091	kinetics-backend	Kinetics API (remapped from 8001)

Deployment Modes

Mode	Config	Description
Bare Metal	`DEPLOY_MODE=allinone`	On-premises. Docker Compose + pre-dumped DBs. ~30 min install.
AWS Cloud	`DEPLOY_MODE=aws`	ECS Fargate, EC2 PostgreSQL (for Bingo), ElastiCache. Scales to zero.
Distributed	`DEPLOY_MODE=platform`	Platform on Dell 1, compute across multiple nodes. add-compute-node.sh.

Pricing

Tier	Price	Workbench	Hardware
Foundation	£2K/yr per member	Not included	1 server
Expert	£20–30K/yr per member	All Workbench tools	2 servers (+£300 hardware)
Trial	£99/30 days	Limited Workbench	Shared

Compute server hardware (£300 one-time) pays for itself in the first week of an Expert subscription. Competitors charge £80–300K/yr for comparable capabilities.

Operational Runbook

Health Checks

# Direct
curl -s http://localhost:8083/health   # combi
curl -s http://localhost:8091/health   # kinetics
curl -s http://localhost:8090/health   # molecular

# Through nginx
curl -s https://app.discoverant.com/workbench-api/combi/health
curl -s https://app.discoverant.com/workbench-api/kinetics/health
curl -s https://app.discoverant.com/workbench-api/molecular/health

Restart Hubs

# Individual hub restart
cd ~/adroit_combi-hub && docker compose restart
cd ~/adroit_kinetics-hub && docker compose restart
cd ~/adroit_molecular-hub && docker compose restart

# Nuclear option (full down + up)
cd ~/adroit_combi-hub && docker compose down && docker compose up -d
cd ~/adroit_kinetics-hub && docker compose down && docker compose up -d
cd ~/adroit_molecular-hub && docker compose down && docker compose up -d

Kill Stuck Jobs

# Find heavy CPU containers
docker stats --no-stream | sort -k3 -rn | head -5

# Restart specific compute container
docker restart molhub-vina     # stuck docking
docker restart molhub-psi4     # stuck quantum calc

Verified Working (8 Feb 2026)

Test	Result	Status
IC50 fit	IC50=0.2777, Hill=0.9844, R²=0.9999	PASS
Library enumeration	4 compounds from scaffold + R-groups	PASS
Conformer generation	3 conformers with energies	PASS
All health checks	`{"ok": true}` on all 3 hubs	PASS
Production URL	app.discoverant.com/workbench → 200	PASS
Development URL	dev.discoverant.com/workbench → 200	PASS

TODO

Priority	Item
HIGH	Set up Dell 2 as dedicated compute server
HIGH	Move Don's containers to Dell 2, set `COMPUTE_HOST=192.168.1.102`
MEDIUM	Consolidate 15 containers → 3–4 (after Don validates)
MEDIUM	Add Workbench API orchestrator (FastAPI :8100) for job queue + SSE progress
MEDIUM	Implement Redis job queue for Heavy/Intensive tier
MEDIUM	"Send to Compound Grid" integration (results → AG Grid columns)
MEDIUM	Get Don's feedback on default parameters + SPR auto-recommendation
LATER	Build deployment installer package (install.sh)
LATER	Implement licence key mechanism
LATER	Add PK/PD module when Don delivers it

Known Issues

Issue	Detail
Kinetics port conflict	Backend remapped to 8091 (8001 conflicts with discoverant-backend-dev)
ADMET integration	May need direct link to :8082 frontend rather than API integration
RAM usage	15 containers use 3–5 GB idling — acceptable short term, Dell 2 resolves it