Outsourcing bioinformatics: 5 dirty secrets

Our customers often come to us after trying out alternative bioinformatics solutions, most commonly employing a bioinformatician of their own. Many have also tested different types of outsourcing options. However, not all of them are optimal for all needs. We present five common pitfalls in buying bioinformatics services.

Instead of service, I got files

Most sequencing service providers will offer a “bioinformatics package” for a fixed fee per sample. It usually entails a few result files from a one-size-fits-all data processing pipeline. Such a service hardly allows for any customization, downstream analysis or support in interpreting and publishing the findings.

This type of "file dump" service may be a reasonable first step into taking a look at the data, but any decent analysis will likely require an actual expert to start the work from scratch.

Ask the service provider:

  • Is the analysis pipeline tailored to my data?
  • Are the results discussed and interpreted with me?
  • Are the analysis methods described transparently to enable their publishing?

With Genevia Technologies, you contract an expert team whose goal is to make you happy by delivering what you actually need. In addition to data analysis, the service includes support in interpreting and publishing your findings and even training your own researchers in data analysis if needed.

Instead of service, I got a software

Many bioinformatics companies are actually software companies. They develop and market software, or platforms. You usually pay a monthly or yearly license to access the software to analyze your own data.

While "biologist-friendly" data analysis platforms can be a great way to dip one’s toe into data analysis, it is not really a bioinformatics solution unless it is accompanied by an expert bioinformatician who understands what exactly the tool does.

One platform warrants a mention here: Galaxy, probably the most used (and free!) tool for setting up ‘omics analysis pipelines without having to code. I once met a one-man bioinformatics core who, not having the time to analyze data for all the research groups, dedicated his time to helping biologists use Galaxy. Not exactly a solution for the lack of bioinformaticians, but certainly very educational!

Ask the service provider:

  • Are there good published papers based on analysis using this software?
  • Is the software transparent with regards to underlying tools and algorithms or is it a black box?
  • Is expert consulting available to tailor the analysis and interpret the results?

With Genevia Technologies, you do not buy software or code (but we are happy to deliver analysis code for publication or re-analysis needs). The only licensed platform we use is Ingenuity Pathway Analysis (IPA) for downstream expression analyses. Otherwise we use and develop R and Python code to enable a truly tailored and transparent analysis workflow.

Instead of service, I got a double-booked post-doc

Some bioinformatics companies are freelance networks. Freelance bioinformaticians may have several customers, and it is up to themselves to ensure they are able to keep them all happy.

Suffice to say, if the freelancer is a full-time postdoc or a PhD student, having access to their evening and weekend hours is not the best predictor of a swift and satisfying project.

Ask the service provider:

  • Does the company list their employees openly and indicate whether they are employed elsewhere?
  • Who is my responsible contact person and what are their credentials?
  • Is the contracted work outsourced to a third party?

With Genevia Technologies, you have a dedicated PhD project manager who is part of our team. We do not outsource work to third parties. See our scientific project managers on our team page.

The service disappeared!

Companies and services may cease to exist. Just as with an employee leaving, a discontinued service does not just stall projects, but often results in someone else having to restart the work from scratch.

Risky service providers include individual freelancers, early startups reliant on external funding, and companies with a focus outside bioinformatics (such as data analysis in general).

Ask the service provider:

  • How long has the service been in operation?
  • Are you reliant on external investors?
  • Is bioinformatics your focus or side hustle?

Genevia Technologies has been in operation since 2011, continuing on its initial mission of providing easy access to the best bioinformatics expertise. We are not a start-up and are not reliant on any external investors to keep us running: our company is fully owned by our founders who have invested all the profits back into our growing bioinformatics team.

“Bioinformatics” was just “informatics”

It is one thing to have to give an employee or service provider a crash course on your subject of study, but it becomes rather inconvenient after realizing they still do not understand, due to a limited grasp of biology.

Bioinformatics is biology, if only dry biology. Many of the best bioinformaticians are trained biologists who've turned to the dark — I mean computational — side. Even the ones with no lab-coat background must understand the basic concepts of the field they are working in, be it cancer research or microbiology.

Ask the service provider:

  • Have you worked in my field of study?
  • Can I learn more about the responsible analyst, or even have a chat with them?

At Genevia Technologies, we select your dedicated project manager based on their expertise. It is often clear from the first contact who is our best bioinformatician for you. In such cases, we are happy to share their resume and even set up a meeting for you to get to know them, all before committing to purchasing the service.

Summary

All of the service and product types discussed above have their time and place. A software can be brilliant and a freelancer with just the right skills may be the best person for you.

However, we believe that a satisfying, long term bioinformatics solution must address the needs of continuity and easy availability of more skills than a single person can master. We've built our team-based service with these needs in mind.

If this sounds like what you need, leave us a message below or continue to download our more comprehensive bioinformatics buyer's guide.

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Antti Ylipää
Antti Ylipää CEO, co-founder Genevia Technologies Oy +358 40 747 7672

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