Do I need bioinformatics support before I even have data?

As a researcher, odds are that you are planning a new research project and have some hypotheses in mind. Perhaps you are thinking of high-throughput omics experiments to test these hypotheses. This is exactly the stage where you want to consult expert bioinformaticians.

What you should know about bioinformatics

The sheer number of available omics measurements can be overwhelming. Exome, whole-genome or panel sequencing? Proteomics or transcriptomics? mRNA, microRNA or single-cell RNA sequencing? ChIP, bisulphite or ATAC sequencing? Not to mention the range of computational analyses for each data type!

In this constantly developing field of bioinformatics, it takes years of training and experience to be able to plan a tailored bioinformatics workflow and to analyze the data to its maximum potential. Computational tools and best practices are evolving all the time, and new software version updates are frequently published. Thus, one must be able to choose the best approaches and tools to match the data and research questions. But the work doesn’t end in selecting the right tool. Generating custom programming scripts to format input and output files, and even developing customized algorithms from scratch, are an everyday part of bioinformatics. The truth is, in the world of high-throughput biology, there isn’t a magical button to push that provides you ready-to-use analysis of the data.

Instead of using thousands of hours to become a specialist in bioinformatics, you could collaborate with those who have already dedicated the time to become experts in handling, analyzing and interpreting high-throughput data, leaving you to concentrate on your own specialism. Leading a research project involving bioinformatics, you do need to know your biological system well and come up with research questions, and any familiarity with bioinformatics is a plus. ”It is never a waste of time to learn the basics of bioinformatics. The more you know, the better, but it is not a requirement for collaborating with bioinformaticians — as long as the bioinformaticians understand you and your research well”, summarizes our scientific project manager Thomas Liuksiala.

The earlier you consult a bioinformatician, the more you get from your data

While it might not be obvious, it pays to involve bioinformaticians from the start when planning high-throughput experiments. An experienced bioinformatician can make sure the planned experiments do indeed allow testing of the key hypotheses, suggest complementary experiments, aid in selecting the best measurement platforms, provide a data analysis plan and can estimate the time and budget for the measurements and bioinformatics.

Considering the data generation and analysis with a bioinformatician from the very beginning helps you ensure that the number of controls and replicates, as well as technical parameters such as sequencing depth, are sufficient for a successful experiment. Naturally, a high-quality bioinformatics plan also helps in securing research funding. Computational analysis can be the most difficult part to cover in a grant application, and it often affects the final funding decision.

Data can never reach the stage where it’s fully analyzed; the question lies in which analysis is relevant for the study and how to analyze.

Antti Ylipää
Antti Ylipää CEO, co-founder Genevia Technologies Oy

Despite all this, bioinformaticians are often involved in the research project only after the high-throughput data has been generated. This can often lead to the full potential of the study not being reached. Most common challenges have to do with data quality, sample size and budgeting. In the worst case, the data is deemed useless and a vast amount of time and money has disappeared into thin air. There is a lot that skilled bioinformaticians can do to mitigate and overcome above-mentioned challenges, but the easiest way to avoid them is to consult computational scientists early on.

Bioinformatics is not a one-(wo)man venture

Like in every field of science, the more bioinformatics develops, the more specialized bioinformaticians become. During their training, a bioinformatician usually becomes an expert in some aspect of computational biology, but not all. This is why utilizing a team of bioinformaticians provides a real advantage.

A successful bioinformatics project benefits from the complementary expertise between data analysts. Any fruitful long term bioinformatics support must involve a team of bioinformaticians, instead of one lonely analyst without the guidance and supervision of senior computational scientists. One bioinformatician may excel in software development, another in creating impressive visualizations and a third may have extensive experience working with just the biological system or disease you specialize in. Professionally managed, such a team is not just better than a one-(wo)man bioinformatics solution, but also quite a bit faster.

Why does bioinformatics take so long in many research projects?

Setting an analysis to run on a server over the weekend does not take a lot of time, but the work does not end nor begin there. Wrangling files into the right format, testing alternative tools, trouble-shooting them, and inspecting the quality of the output, is labor-intensive. This is where an experienced bioinformatician or, rather, a team of bioinformaticians with complementary expertise, can truly distinguish themselves by tackling the otherwise time-consuming tasks with routine. The most demanding challenges involve separating artifacts and noise from true biological signals, and communicating the findings with the aid of clear visualizations. Finding the relevant information from the output of computational analyses tends to require more brainwork than compute time, and a great deal of experience. By utilizing an expert team of bioinformaticians instead of relying on one individual, you can ensure that the project doesn’t get delayed due to the lack of resources and/or experience.

When planning your next omics project, hopefully you feel more inclined to consult bioinformaticians! Get more familiar with our business model, bioinformatics as a service, and read more about the benefits of the bioinformatics consulting meeting. If you would like to plan your next research project with us, contact our CEO Antti Ylipää directly or leave a message below.

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