Questions & Answers

At what stage can we start working together?

At any stage. You do not need an ongoing project or a defined question to make contact. Some clients come to us before a single sample has been collected – to design the study, choose a sequencing strategy or make the case for funding. Others arrive with data already in hand and a specific analysis to complete. Others still have results from an analysis they ran elsewhere and need a second opinion, an integration step or support getting the work into a paper.

If you are not sure where your project falls, that is fine too. Tell us where you are and what you are working towards, and we will work out together where we can be useful.

What do I need to provide to get started?

Whatever you have. If you are at the design stage, a question and a rough sense of your sample numbers is enough to have a useful conversation. If you have existing data, the format matters less than you might think: raw sequencing reads, processed count matrices, assembled genomes or partial results from a previous analysis are all workable starting points.

If your data is messy, incomplete or in an uncertain state, say so – that is not a reason to wait before making contact. Part of the initial conversation is working out what you have and what it can support.

Do you work with academic and commercial clients?

Yes, both. We work with university research groups, public research institutes and commercial clients including biotech and agricultural industry. For commercial projects, we sign an NDA on request before any data or unpublished material is shared, and deliverables are structured to meet the documentation requirements of an R&D environment as readily as an academic one.

Are you set up to take on a project like mine?

OMIKS has been operating since 2023. The people working on your project have carried research questions through to a conclusion many times over, across a wide range of biological systems and question types. That breadth is what lets a project be scoped realistically, a result interpreted correctly and a conclusion defended, whatever the specifics turn out to be. On larger projects, we combine forces. Our compute scales with what the work needs, not the other way round.

If a project calls for a specific platform or method neither of us has direct hands-on experience with, we’ll say so early rather than approximate it (see “What if my project isn’t the right fit for you?” below).

Do you only take on complex projects?

No. Some questions have a known pipeline and a clean answer – we run those properly. Others don’t have an obvious answer yet, and that’s where most of our work sits. We scope honestly either way, and price accordingly.

What if my project isn’t the right fit for you?

We’re upfront about it. If your project needs something we can’t provide, we’ll say so early – the initial conversation costs nothing either way. Sometimes that means pointing you elsewhere; sometimes it means narrowing the scope into something we can help with.

How does pricing work?

Engagements are priced to fit and scale. As a rough sense of scale: a defined analysis with a clear deliverable typically runs from the low thousands of euros; larger or evolving work scales up from there depending entirely on scope. Smaller, well-scoped questions are welcome too – pricing follows what a project actually needs, not a minimum engagement size. If yours is substantially bigger, tell us and we’ll be straightforward about whether it’s a good fit.

We work with two models depending on the nature of the project.

Fixed project quotations work well when the scope is clear from the start – for example, a defined differential expression analysis, a genome assembly with annotation or a specific set of analyses with a written report. You know exactly what you are getting and what it costs before we begin.

Hourly billing is used for exploratory or evolving work – projects where the questions develop as the data comes in, or ongoing collaborations where requirements shift over time.

Every quotation sets out precisely what is included: which analyses, which deliverables and where the scope ends. Anything beyond that is discussed and agreed before additional work begins. Work begins on a paid basis, including preliminary analysis for a grant application still being written.

Payment terms depend on project size and whether we have worked together before. For new clients on larger projects, partial payment in advance may apply. For established clients, invoices are tied to milestones or project completion. All terms are agreed in writing before work starts.

Projects range from a single focused analysis to multi-year collaborations. They begin with an initial free consultation to understand your objectives and define scope. Once this is established, we issue a written quote for the proposed work.

How long do projects take?

Project timelines depend entirely on scope, and scope is always agreed in writing before work begins. A focused single analysis with clean data and a well-defined outcome, for example a differential expression analysis, can be complete within a week, reads to report. Defined projects with a fixed deliverable set typically run several weeks to a few months. Longer collaborations – where questions develop as the data comes in, or where ongoing analytical support is needed – run across months or years; our longest current collaboration is in its third year.

If your project has a hard deadline – a grant submission, a conference, a regulatory milestone – tell us upfront. We’ll confirm honestly whether we can meet it, and if we can’t, we’ll say so immediately rather than let you find out later.

Who owns my data and results?

You do. All data, results, figures, code and any other outputs belong entirely to you. We make no intellectual property claims on any part of the work.

Projects are treated as confidential as standard. Your data is never used for our own research, benchmarking or publication without your explicit written consent.

Where we publish methodological work – new pipelines, analytical approaches or similar – this draws on our own independent research, not on client data.

Will I receive full code and documentation, or just the results?

Whichever you prefer. Every project is documented and version-controlled internally as standard practice, the same discipline as a good laboratory notebook, so the work is always reproducible and retrievable regardless of what you receive. Some clients want the full code, the reasoning behind it and a record of what was tested and rejected. Others just want the results and a written interpretation. Either way, the underlying work meets the same standard, and nothing is ever undocumented or dependent on one person’s memory.

Where is my data stored and is it secure?

At a glance:

• Data storage: within the European Economic Area
• Sub-processors: EU-based
• NDA: available on request before any data is shared
• DPA: available on request, GDPR-compliant
• Data retention: up to 90 days after project completion, then deleted unless you request otherwise in writing

Access during the project is controlled and can be structured to meet your institutional requirements. When the project is complete, all outputs are transferred to you.

Can you work with human or sensitive data?

Yes. We work with human genomic and other sensitive data under appropriate legal agreements. Before any data is shared, we sign a Data Processing Agreement in line with GDPR requirements – either our standard template or yours. All data is stored on infrastructure based in the European Economic Area, with EU-based sub-processors throughout, and access is controlled throughout the project.

If your data is subject to ethics committee approval or institutional oversight, bring that documentation to the initial conversation. We are familiar with the constraints these place on data handling and will work within them.

How does communication work during a project?

Updates are tied to milestones – at each stage you receive a progress report, any intermediate results and a clear picture of what comes next. Beyond that, we adapt to how you prefer to work. Some clients want regular meetings to discuss findings as they develop; others prefer to receive the final outputs and engage only when something needs input from them. Both are fine, and we agree the cadence at the start of the project.

Either way, you are always dealing directly with the people running the analysis – not an intermediary. If something unexpected comes up mid-project, you hear about it promptly and directly.

What if the results are negative or inconclusive?

The analysis is completed and documented to the same standard regardless of outcome. A null result – no significant differential expression, no pathogen detected, no clear separation between groups – is not a failed analysis. It is a finding: it tells you that the effect is absent at this scale, below the detection threshold of the current design or requires a different approach to resolve. That is useful information, and it is documented as such.

If results are inconclusive, we discuss what that means in practice – whether the question is answerable with more data, a modified design or a different method. You leave the project knowing where you stand and what the options are, not just what the pipeline returned.

What if the deliverable isn’t what I expected?

Because scope is agreed in writing before work begins, there is a clear reference point for what the deliverable should be. If something in the output falls short of what was agreed, we address it – that is part of the engagement, not an additional cost.

What we cannot guarantee is the biological outcome: whether a result is significant, positive or confirms a hypothesis is determined by the data, not the analysis. What we do guarantee is that the analysis is sound, documented and matches what was scoped. If expectations and scope have drifted apart during a project, we would expect to have flagged that before delivery rather than at it.

What if the project scope changes?

Project aims can and do change – that is a normal part of research. Small adjustments are typically absorbed within the existing agreement. Larger changes, such as new analyses or a substantially different direction, are discussed and re-quoted before we proceed. For hourly projects, changes simply continue under the same billing model.

We flag scope changes early rather than absorbing them silently and invoicing at the end. You will always know where you stand.

What if I need to pause or cancel?

You can pause or cancel at any point. If a project ends early, you are invoiced only for work completed and any computational or operational costs already incurred. Everything produced up to that point is yours. Projects can be resumed subject to availability.

Can you help with grant applications?

Yes. We support grant applications at several levels: developing the analytical approach and methods section, generating preliminary data and figures to support feasibility and helping frame the computational component of the proposal in terms that reviewers find credible. If you have a research idea that is not yet a funded project, that is a reasonable place to start a conversation – preliminary data generated now is often what makes an application competitive rather than merely plausible. All work and data related to unfunded projects is treated with complete discretion.

Can you help with manuscript writing?

Yes. We can support the full arc of manuscript preparation – experimental design, data analysis, figure development, writing methods and results sections and preparing for submission.

Because manuscripts develop over time and go through revision cycles, all manuscript-related work is billed hourly. This keeps things fair on both sides when the scope shifts during peer review or revision. We agree the initial scope – datasets, figures and manuscript structure – before starting, and revisions or additional analyses are covered under the same model.

Do you expect co-authorship or acknowledgement?

No. Authorship and acknowledgement are entirely at your discretion. We do not request or expect either as a condition of engagement. How our contribution appears – or does not appear – in your publication is your decision.

How do we get started? Is there a cost to the first conversation?

The initial consultation is free of charge. We meet online to understand your data, your question and what a good outcome looks like. From there we put together a written scope and agree terms before anything begins. We work in English.

We discuss questions at any stage, formed or not – early conversations often shape the project considerably before any work is commissioned.

Start a research enquiry or email enquiries@omiks.it with a brief description of your data, your question and your timeline.

We need to register you as a supplier. What do we need?

We operate under Italian law and provide a VAT number on request. We issue formal invoices for all work.

We support supplier registration and institutional vetting processes. If your institution has specific requirements – supplier questionnaires or data processing agreements – contact us and we will work through them with you.

We sign an NDA on request before any data or unpublished material is shared. For projects involving personal data – including human genomic data – we can also sign a DPA in line with GDPR requirements. If your institution has standard templates for either, send them through and we will review them.