Bioinformatics hurdles in Translational Research: A perspective

by | Mar 11, 2022 | Bioinformatics, Resources | 0 comments

Translational research often involves collection of large datasets and performing elaborate analyses. Wet lab researchers often find the world of bioinformatics overwhelming and are not sure where to start, or even what benefit it can bring to their research outcome and impact. My name is Lijing Lin, and I recently joined the Translation Manchester team as a Translational Research Bioinformatician. I come from a computational mathematics background; however, over the past seven years, I have worked as a postdoctoral researcher across different biological research groups, and researched on a variety of bioinformatics and health informatics projects. Reflecting on my own transition into bioinformatics, as well as through close interactions with my wet lab colleagues in different areas of biomedical research, I would like to outline here some of the common bioinformatics hurdles usually faced by data generating labs, which, from my perspective, are a significant bottleneck for translational research. Later, I also suggest some possible solutions.

Training needs

Bioinformatics needs are ubiquitous in modern day biology and biomedicine labs, and bioinformatics expertise is required at different stages of the project lifecycle. Project progression can be hampered if there is a lack of bioinformatics expertise (students or postdocs) within the research group. Even the existing expertise could prove short-term since the students/postdocs may move on.

A biologist might not be entirely sure what bio-informatics training they require to address the question they are asking. Moreover, with the increasing complexity in the data, automated methodologies such as machine learning (ML) methods are becoming increasingly critical for research. However, without adequate training data-generating researchers might not be able to spot what elements of the data they generate can have ML applied to them. Hence, regular bioinformatics training for data-generating researchers is absolutely necessary. Short-term solutions include training programmes for core skills such as programming and statistics, and targeted workshops for more specialised training such as omics analysis workflows and machine learning in bioinformatics. For more strategic long-term training policies, consideration should be on how to effectively incorporate bioinformatics across the biomedical curriculum for postgraduate or even undergraduate students in order to build capacity.

The Informatics Training Scheme provided by Translation Manchester presents one possible solution here:  it allows researchers to enrol in units within the postgraduate taught courses provided in the Faculty of Biology, Medicine and Health (FBMH) to train and upskill translational researchers in wide ranging informatics areas. Stay tuned to hear the launch of the Informatics Training Scheme for 2022.

Supervision of computational PhDs/postdocs

Principle investigators (PIs) without a computational background could face difficulties in supervising computational PhDs/postdocs within the lab. In light of the established ‘Team Science’ concept – output-focused research involving two or more research groups – as well as the importance of Team Science in Translation we recently spoke about, one possible solution is joint supervision of PhD/postdocs with computational PIs. This is already in place for some PhD programmes within FBMH but more needs to be done in this space. In the long run, creating a culture of continuous collaboration between wet-lab and computational PIs will be beneficial. We should encourage such collaboration to start as early as project development phase, and enhance close collaboration in activities including managing scope and expectations, experimental designs, data management, analytical study planning and validating, and delivering scientific outcomes (publishing papers or informing further experimental validations).

Effective communication with central bioinformatics support

For some research projects, bioinformatics support is primarily received through the institution-level shared core facilities. One obstacle in research progression is in effectively communicating between bioinformaticians and data-generating researchers.  It is essential for researchers to clearly convey the research objectives and to explain the data generating procedure, sample quality metrics and potential issues. For the bioinformaticians, it is equally important to explain how the proper analytical approaches are designed to address the goal, data quality issues, how the go or no-go decisions are made in the analysis, and how to interpret the results including graphs and numbers. One way forward is, for example, to hold regular bootcamps with core facilities for them to explain their portfolios and share information about work pipelines.

How to move forward and what we can offer

In order to move forward and help the translational research progression, we as bioinformatics support at Translation Manchester are going to facilitate this training and capacity building, both short-term and long-term. We are happy to talk to you, and help identify the major hurdles, choose suitable computational tools/analytical skills for data analysis, and signpost appropriate training. We also help discover various collaboration options. For example, when PIs want to include bioinformatics expertise on grants, we can act as a point of contact to help them find the right people to collaborate with. At Translation Manchester we are about facilitating translational research, but also about helping researchers from different disciplines (e.g., biologists, mathematicians/bioinformaticians/biostatistician) to communicate with each other by “translating” respective languages, so no one will get lost in translation! Regarding specific trainings and support, we will collate and communicate best practice and available resources. These will be covered in detail in my next bioinformatics blog post very soon – stay tuned!

If you have any questions on the support we can provide, get in touch by clicking the link below: