Bioinformatics: scalability, capabilities and training in the data-driven era

Maria Victoria Schneider, Rafael C Jimenez, Bioinformatics: scalability, capabilities and training in the data-driven era, Briefings in Bioinformatics, Volume 20, Issue 2, March 2019, Pages 735–736, https://doi.org/10.1093/bib/bbz053

Not too long ago, in 2013, we worked on a special issue for Briefings in Bioinformatics Internationalization, its interdisciplinary nature and the various emerging efforts in multi-level bioinformatics training and education. The benefits of these efforts are becoming evident, with the community of experts delivering training and services becoming better organized and increasingly interconnected.

Training plays a fundamental role to overcome the skills gap amongst life scientists, especially in a fast-changing data-driven and multidisciplinary research landscape. Thus, training is becoming a key pillar within organizations aiming to support researchers. Though many of these organizations have their own training strategy we can already see how concrete agreements and collaborations between them are being established to face common problems. The increasing cooperation among bioinformatics organizations and the training community is leading to a better structured effort to scale and increase capabilities to better understand and cater for the training needs of both the life science researchers and their trainers.

The research infrastructures and bioinformatics societies highlighted in the articles of this issue are an example of this ecosystem of interconnected organizations. The SIB Swiss Institute of Bioinformatics (SIB), the German Network for Bioinformatics Infrastructure (de.NBI), the Dutch Techcentre for Life Sciences (DTL) and the EMBL Australia Bioinformatics Resource (EMBL-ABR) in Australia described in this issue are national research infrastructures of bioinformatics service providers with the aim of supporting life science researchers. They are federated infrastructures engaging several national partners with a defined programme and an agreed set of priorities.

SIB, de.NBI and DTL are also organized at a European level, sharing common objectives as part of a broader effort named ELIXIR. ELIXIR is a European intergovernmental organization encompassing more than 20 countries including 180 organizations. It coordinates and develops life science resources across Europe so that researchers can more easily find, analyse and share data, exchange expertise and implement best practices. Training is one of the five core ELIXIR’s platforms. The ELIXIR Training Platform is focused on the development and implementation of a common training strategy. In this, the ELIXIR training platform relies on the expertise of its members, collaborates with other national research infrastructures such as EMBL-ABR and establishes key partnerships with training organizations including GOBLET and Data Carpentry.

Bioinformatics societies also play an important role in education, usually having training and its promotion as part of the remit of their activities. Similar to research infrastructures, bioinformatics societies have links with other societies and training organizations.

Despite these efforts, and their broad scope, the training needs of life scientists will require an even more concerted and global response from stakeholders involving not just research infrastructures and bioinformatics societies but policy makers, funding agencies and educational organizations.

In this issue of Briefings in Bioinformatics we have brought together the experience of training initiatives across this range of settings:

Baillie-Gerritsen et al. provide an overview of Bioinformatics in Switzerland the role of SIB to support bioinformatics and research. SIB is a well-established distributed research infrastructure with more than 19 years of expertise in the field of Bioinformatics. It is comprised of 19 national partners organized in 12 competency centers and 65 research and service groups. Their services, technical activities and training are grouped into thematic areas including gene and genomes, proteins and proteomes, medicine and health, evolution and phylogeny, structural biology, systems biology and bioinformatics infrastructure.

Tauch et al. present the de.NBI. de.NBI is a distributed infrastructure formed in 2015 to provide bioinformatics services and training as well as foster national and international cooperation. It has 30 project partners and is organized in 8 service centers: the Center for Microbial Bioinformatics (BiGi), Bioinformatics for Proteomics (BioInfra.Prot), the Center for Biological Data (BioData), the Center for Integrative Bioinformatics (CIBI), the de.NBI Systems Biology Service Center (de.NBI-SysBio), the German Crop BioGreenformatics Network (GCBN), the Heidelberg Center for Human Bioinformatics (HD-HuB) and the RNA Bioinformatics Center (RBC).

van Gelder et al. provide a historical overview of bioinformatics in the Netherlands emphasizing the rich legacy of expertise in the field Bioinformatics harnessed and promoted by the DTL. DTL was formed in 2013 with a strong focus on organizing expert data stewardship training in the Dutch life sciences. It includes 50 life science institutions organized in more than 120 expert groups focus on scientific domains such as health and technology areas like genomics.

Schneider et al. introduce EMBL-ABR, a distributed national research infrastructure providing bioinformatics support to life science researchers in Australia. EMBL-ABR was established in 2016 and comprises 10 geographically distributed national nodes with 1 coordinating hub. The activities of EMBL-ABR are focussed in six key areas, aligning with comparable international initiatives such as ELIXIR, CyVerse and NIH Commons. These key areas are Tools, Data, Standards, Platforms, Compute and Training.

De Las Rivas et al. give an overview of the history and current state of the research in bioinformatics and computational biology in Latin America. It also introduces the role of SoIBio as a scientific and professional society to promote research and development of bioinformatics and computational biology in the international region of Ibero-America. SoIBio was formed in 2009 and includes representatives from 22 Ibero-American countries.

Attwood et al. summarize the work of several surveys evaluating bioinformatics skills gaps. It concludes there is still a considerable training deficit in the life science community that needs to be overcome. It also draws special attention to the need to embed earlier bioinformatics in educational programmes and the need to train future trainers. Organizations like ELIXIR and GOBLET have been instrumental to improve training in life sciences, yet the main challenges in bioinformatics training require the support and collaboration of lecturers, teachers, trainers, policy makers and funding agencies across the world.

Via et al. present the results of a pilot for a pan-European Train-the-Trainer bioinformatics programme. If focuses on how to increase bioinformatics capacity and competency across the life science community helping bioinformatics instructors to better design, develop and deliver high-quality training. It emphasizes the need to establish a network of trainers and instructors, and it links with the efforts of organizations like GOBLET and ELIXIR.

In any system it is desirable to know the number of process variables that can be regulated. The Degrees of Freedom Analysis is a method that can be used for this purpose and that can be applied to make decisions for bioinformatics training and educations as demonstrated in the article from Tractenberg et al.

Ragan et al. present a review of specific phylogenetic inference methods. Research infrastructures rely on the expertise of their partners and their national strengths to provide services and support. This review done by one of the EMBL-ABR partners presents an evaluation of conceptual foundations of alignment-free phylogenetics approaches contributing to research in phylogenomics and gene transfer.

Maria Victoria Schneider

Honorary Associate Professor

University of Melbourne, Australia

Rafael C Jimenez

Chief Technical Officer

ELIXIR