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Bioinformatics Training Network Tries to Evolve as Genomics Advances


CHICAGO (GenomeWeb) – With demand for bioinformatics expertise continuing to outstrip supply, one small organization is working to serve as a hub for training organizations and to harmonize curricula for educating the next generation of professionals.

"We're a network of networks, essentially, a network of organizations and individuals who have education and training in bioinformatics at the core of their responsibilities and interests," Michelle Brazas said of GOBLET, which stands for the Global Organization for Bioinformatics Learning, Education, and Training. Brazas, who serves as secretary of GOBLET, is informatics program manager at the Toronto-based Ontario Institute for Cancer Research.

Membership includes large training organizations, including the European Molecular Biology Laboratory's European Bioinformatics Institute, in Canada, the Swiss Institute for Bioinformatics, the International Society for Computational Biology, and many individual teachers of bioinformatics, according to Brazas.

Incorporated in the Netherlands but run as a virtual organization without a true headquarters, GOBLET was founded in 2012, superseding the Bioinformatics Training Network — which Brazas said was Eurocentric — and bringing in more groups from North America, Asia, and beyond. While it is certainly a train-the-trainer type of organization, GOBLET strives to be more.

"As a group, any one individual organization always felt that they were alone in the training sphere. Together, you realize that you are not alone. In fact, there are quite a lot of you," Brazas said in an interview at the annual Intelligent Systems for Molecular Biology (ISMB) conference here this month.

"We come together to enhance our own skills in training bioinformaticians to keep up to date on the topics to talk about minimum requirements in the curriculum in bioinformatics, minimum standards for training materials, for example," Brazas explained.

"Education is constantly moving forward," Brazas added. "[GOBLET is about] staying aware of how we can best keep ourselves on top of our field of education and training, staying aware of current topics and needs in bioinformatics, and working together to address those needs and to address our own training."

GOBLET has tried to evolve as bioinformatics and genomics have changed. Initially, the group's constituency was almost entirely laboratory-based. Today, some GOBLET members train clinical groups on the use of informatics tools, according to Brazas.

"The audiences are changing. More clinicians are becoming aware of bioinformatics. While they may not need the depth as other audiences, the awareness is there because if a patient shows up with their genetic variants from a particular panel, they want the clinicians to be able to discuss that," she said.

At the same time, the level of training and the topic areas have changed.

Initially, the GOBLET audience consisted of undergraduates, graduate students, and informatics professionals looking to enhance their skills, while training material focused on general informatics, general genomics, and general proteomics.

As universities began to offer undergraduate bioinformatics courses, the need for supplementary undergrad courses waned. "It forced the topic areas to shift to more advanced topics [like] more advanced analyses in parallel with new technologies," including next-generation sequencing, Brazas said. "I think a lot of the organizations in GOBLET experienced that shift from general to more advanced topic areas."

Meanwhile, member organizations have seen more activity in data management training. GOBLET itself does not develop software, but it works with its members that do so.

"You can teach about single-cell analysis, but if there is nothing to solve the problem about how to do the analysis, it's really quite difficult to manage," Brazas noted. "We are talking about transcriptomics or single-cell genomics."

She also said that there is more interest in managing long-read sequencing data from nanopore sequencers, as well as in data integration from both lab and clinical sources.

Another current activity for GOBLET is an attempt to standardize training materials worldwide. The group works with ISCB's curriculum task force, among others, to develop curriculum guidelines for teaching bioinformaticians. "That has led to collaborations with the groups doing data science curricula," Brazas noted.

In that area, GOBLET is working with Bioschemas, a community initiative that encourages people and organizations in life sciences to structure information on their websites for easier indexing, searching, and retrieval.

"Because GOBLET represents so many groups globally, it's easy to translate across everybody very quickly through the network, and everybody has a voice in those standards, and it's readily adopted because everybody had participated in that standard development," Brazas said.

Interestingly, as bioinformatics training and continuing education have moved to a higher level, some members have their eyes on a younger crowd. At ISMB, the education track included discussion of getting bioinformatics into science curriculum as early as high school.

Brazas noted that high school biology students are already exposed to bioinformatics, even if they or their teachers do not realize it.

In researching a medical condition, students might start with Wikipedia, Brazas suggested. "They're going to look up sickle cell disease. They're going to get to a Wikipedia page and from a Wikipedia page, they're going to end up maybe on NCBI [National Center for Biotechnology Information] and GenBank, so it's a very natural hop," she said.

"They are already exposed. It's just a matter of pointing out that exposure and pointing out the topic area of bioinformatics at that level."