JapalityLimited · Hong Kong

Collaboration

Scoped software.
Useful outcomes.

Japality Limited works with universities, research groups, and organisations on project-based AI systems, scientific software, data workflows, and product engineering. Each enquiry is reviewed for fit; work begins under a written agreement with clear deliverables.

Send an enquiry Illustrative workflow
01

AI systems

Agents, tooling & LLM workflows

Software that makes models useful in day-to-day development and research environments—agents, routing, evaluation loops, and workflow design. Public examples include BeanAlis, BeanAlis GUI, JapalityBean, Japalitynil, and JNL-X.

Typical project components

  • Terminal and CI coding-agent design
  • Model routing, evaluation, and verify gates
  • LLM workflow DSLs and orchestration
  • Tool use, MCP integrations, and guardrails
  • Retrieval pipelines and context packaging
  • Documentation, packaging, and handover
Note

Model outputs can be wrong. Validation, access control, and acceptable-use policy stay with the partner.

02

Scientific software

Data, methods & computational tools

Paid, scoped computational analysis, reproducible workflows, visualisation, and domain-specific utilities—including sequence and NGS software when the project needs it. Public tools include MicroBioLens, JapalitySplice, and JapalityAligner. Wet-lab work stays with the partner’s facility or their contracted laboratory.

Typical project components

  • Exploratory data analysis and review
  • Workflow automation and pipeline design
  • Sequence and NGS software utilities
  • Visualisation and data packaging
  • Reproducibility checks and method notes
  • CLI tools and file-format utilities
Data

Do not send biological samples, cultures, sensitive datasets, credentials, or confidential files in an initial email. If a project proceeds, authority to use the data, transfer method, access, retention, and deletion are agreed in writing first.

Illustrative mixed-sample workflow
03

Product engineering

Apps, utilities & maintainable delivery

From a compact research utility to a polished mobile product, we turn a well-defined technical process into software people can run repeatedly—including store-ready apps when that is the right distribution path.

Typical project components

  • Mobile and desktop prototypes
  • On-device processing where it helps
  • Developer tools and calculators
  • Workflow automation and file handling
  • Algorithm integration and performance work
  • Technical documentation and handover
Fit

Prototype and research software should match its stated purpose. Production, security, and quality expectations need to be written into the project scope when they matter.

Illustrative engagement

Computational screening around a mixed microbial sample.

A worked example of a commercial software project—not a completed client case, not a laboratory service, and not a certified identification.

Suppose a research or industry partner already holds a mixed culture from their own fermentation or environmental R&D and wants computational help to see which organisms in a chosen reference panel have sequence-read support, then use their bench to isolate colonies and obtain an orthogonal marker sequence.

Japality Limited is a Hong Kong software company. We do not operate a laboratory and do not accept, culture, store, or ship biological materials. The partner provides the facility, equipment, reagents, biosafety arrangements, and contracts with licensed sequencing providers. Japality is paid for software configuration, computational analysis, method notes, and handover under a written agreement.

The interactive diagram needs JavaScript. The written method below is complete without it.

Illustrative responsibility map. Green nodes are Japality software work. Amber nodes stay at the partner’s facility. Blue nodes are the partner’s contracted sequencing provider.

What the partner buys

Software, analysis, and a written method.

  • Scoped computational analysis of partner-provided sequence files
  • Custom MicroBioLens panel setup and a classification report
  • In silico primer-specificity review with japality-primer
  • Method notes another scientist can review and rerun
  • Optional tool packaging, training, or a commercial licence

What the partner keeps

Samples, bench, and legal responsibility.

  • Physical samples, cultures, isolates, and shipping
  • Laboratory space, equipment, and reagents
  • Contracts with sequencing or other wet-lab vendors
  • Biosafety, permits, and lawful sample origin
  • Interpretation for product, clinical, or regulatory use
  1. 01

    Partner facility

    Start from a sample the partner already holds lawfully

    Example: a mixed fermentation or environmental sample from the partner’s own R&D. The partner warrants origin, any required permits, and that sharing digital sequence data is authorised. Japality does not collect field samples and does not receive the physical material.

  2. 02

    Partner’s sequencing provider

    DNA extraction and NGS stay with a laboratory the partner contracts

    The partner (or their vendor) extracts DNA and generates shotgun or 16S read files. Japality is not the sequencing provider and does not take custody of tubes, plates, or extracts.

  3. 03

    Written agreement, then files only

    Share digital FASTQ after scope, licence, and confidentiality are signed

    Work starts only under a written agreement covering purpose, data rights, transfer, retention, and fees. Do not email sequence files, credentials, or confidential attachments in a first enquiry.

  4. 04

    Japality software

    Classify reads against a partner-chosen panel with MicroBioLens

    MicroBioLens is a custom-panel shotgun / 16S classifier. It reports which organisms in that panel have read support. It does not discover every unknown taxon, isolate a living culture, or confirm a strain. The partner chooses the panel (for example common fermentation-associated taxa plus any hypothesized targets); references are fetched from public sources such as NCBI as the tool allows.

  5. 05

    Partner facility

    Colony isolation happens on the partner’s bench

    If a living isolate is the goal, the partner cultures and picks colonies using their own containment, media, and equipment. Many organisms detected as DNA will not grow on standard plates. Isolation is optional, may fail, and is never performed by Japality.

  6. 06

    Japality software

    Review candidate primers in silico — japality-primer does not design them

    The open-source japality-primer CLI is an in silico specificity checker (PCR simulation, multi-genome matrix, read scanning). Primer candidates may come from the partner, published assays, or design-exploration software such as the Japality Primer app. Wet-lab PCR, optimisation, and validation stay with the partner.

  7. 07

    Partner facility

    Use PCR, if wanted, to screen colonies before sending a few for sequencing

    The partner runs PCR on their isolates or samples. A computational specificity table is not a wet-lab result. Primers can miss the target, amplify near neighbours, or fail on real DNA.

  8. 08

    Partner’s sequencing provider

    Selected isolates can go for 16S or another agreed marker as an orthogonal check

    16S (or a similar marker) can support genus- or species-level placement for many bacteria. It is not strain confirmation and does not, by itself, prove purity, viability, safety, or function. Strain-level questions usually need whole-genome comparison or another agreed method—and still belong to the partner’s laboratory path.

Engagement model

What we clarify before work begins.

A written scope protects both sides and keeps delivery honest.

01

Purpose & users

Who the software is for, what success looks like, and what it must not be used for.

02

Inputs & access

Data types, ownership, permissions, and how materials will be shared.

03

Methods & validation

Documented approaches, known limits, and partner-side review where needed.

04

Security & retention

Transfer, access, processing location, minimisation, retention, and deletion.

05

Deliverables & IP

Outputs, documentation, ownership, licences, and reuse rights.

06

Commercial terms

Milestones, fees, timing, change control, and acceptance.

A useful first email includes

Enough context to assess fit

  • Your organisation and role
  • The problem in plain language
  • Whether it is AI, scientific software, data, or product work
  • The expected deliverable and timeline
  • Any hard constraints (platform, language, privacy, budget band)

Please hold off sending

Until terms are agreed

  • Biological samples, cultures, extracts, or isolates
  • Large or sensitive datasets by email
  • Personal, health, or human sequence records
  • Production credentials or private keys
  • Third-party confidential material without clearance

Project enquiry

Tell us the problem you want solved.

A short, non-confidential overview is enough to start a conversation. If there is a fit, fees, deliverables, and responsibilities are set in a written agreement before work starts.

info@japality.com See our privacy notice for how we handle contact data.