CASP a new bridge between life science and data science

Kate Bennett, Department of Chemistry, is the CASP platform manager.

ImageDavid Nilsson

The goal is to help researchers extract the most out of their experimental data,  being able to draw valuable biological and chemical conclusions.

What is the CASP platform?

“The platform  has recently been launched within the framework of the Computational Life Science Cluster (CLiC) at Umeå University. CASP currently consists of a small group of data scientists, biochemists and analytical chemists. Together, the group has strong expertise in  data analytics, in addition to wide domain knowledge arising from active engagement in multiple projects in the omics area and beyond.  It's  great that we can all work together using  our complementary expertise. This allows us to gain a full understanding of the customer's needs, not only in terms of the data analysis, but also in how the data was generated and  equally important, the biology behind the project.”

What type of analyzes can be done at CASP?

“CASP offers a wide range of data analysis tools allowing you to explore trends, patterns, relationships and even  predictions within  large  data sets. The ultimate goal is to help researchers  make the most out of their experimental data,  being able to draw valuable biological and chemical interpretations.”

“We provide tools and solutions within AI / deep learning, machine learning, multivariate data analysis (MVA), univariate statistics and statistical experimental design. Our main focus is MVA which is a statistical technique used for the analysis of data involving more than  two types of measurements or observations. A perfect example would be the analysis of metabolomics data, which explores  the abundance of many metabolites and often from several subjects.  These types of methods allow you to explore relationships in your data and pinpoint variables (in this case metabolites) that are altered  under specific conditions such as disease. Examples of MVA techniques include principal component analysis (PCA), orthogonal projections (OPLS) to latent structures and multiblock data analysis (O2PLS/OnPLS). A complete list of the analyses we provide can be found on our website.”

“We also have tools to help with the design of your project. For example, when choosing a representative set of samples to be analysed from a much larger cohort, minimising any bias in the selection.”

Which researchers and research areas are the target group?

“Our primary target group are life science researchers from multiple  areas including health, medicine, pharmaceuticals , agriculture and the food science industries to name a few. One of our goals in the near future is to become an  extended support for researchers who use Umeå University's experimental platforms such as the Swedish Metabolomics Centre (SMC) and the Vibrational Spectroscopy Core Facility (ViSp). These impressive state-of-the-art facilities generate huge amounts of data and it can often be difficult to know the best way to analyse and interpret this data into a biological or chemical context. This is where we at CASP want to come in to help to become a bridge between life and data  sciences.”

“Although we are primarily a service platform, we also aim to train researchers in the methods we use. The goal is that they can then walk away with the confidence to use the tools themselves for future studies.”

What do you do in your role as coordinator?

“My role as coordinator is very varied, which is something I enjoy and manages to keep me on my toes! As part of CASP, my daily tasks include having meetings with customers, planning activities and projects within the platform, writing reports and even  stretches to budget planning. PR for the platform has been an important role during our start-up phase and reaching out to potential customers, whether that be via e-mail, telephone, social media or by holding seminars at various departmental meetings.”

“Another side  to my work is  running metabolomics projects. This gives me the opportunity to get back into the lab, which I have always loved to do.”

As a chemist, what is your background and how did you end up in Umeå?

“My background is in both biochemistry and mass spectrometry. Over the years, my research has focused on the use of omics methods to understand disease mechanisms, with a particular focus on rare genetic disorders and age-related diseases.”

“After my doctoral degree at University College London, I took the exciting step of moving to Umeå as part of a Marie Curie ITN project where I worked for many years at a small and medium-sized company, specializing in metabolomics and clinical-based studies. During this time, we had strong connections to Umeå University, especially to the Swedish Metabolomics Centre and the Department of Chemistry. The expertise I gained in both metabolomics and data analysis, led to my role as Research Coordinator as part of Johan Trygg's group at the Department of Chemistry and to my involvement in CASP.  Although my plan was originally to stay in Sweden for two years, I am still here ten years later and now see Umeå as my home - even in the depths of winter!"

Katie bennett together with the personnel of the Computational Analytics Support Platform (CASP), Umeå University.

ImageDavid Nilsson