Bioinformatics has been defined as ‘
a field that solves problems in the biological sciences using computer science concepts and methods’ [1
]. A similarly broad definition of bioinformatics comes from an interview with Francis Collins in which he describes computational biologists as ‘
jointly trained in understanding biology in all of its complexities, but they’re also very capable at computational analysis of huge data sets
] In many ways these are excellent descriptions of bioinformatics today, because of their inclusivity. Computer science, software development, statistics, data management and a wide-range of biological sciences—including computational, experimental, systems and theoretical biology—are all contained in these definitions.
Interest in bioinformatics education followed quickly behind the establishment of bioinformatics as a field of study. If one searches PubMed for the term ‘bioinformatics’ over 70
000 articles are retrieved [4
]. The earliest of these are from the mid-1980s but as discussions, and then expectations, about the completion of the Human Genome Project increased, so too did the development of bioinformatics as a field [5–7
]. The initial formats for bioinformatics education were often partnerships between forward thinking individuals—molecular biologists (able to write programming code) collaborating with computer scientists to determine best practices; a biology professor and an excited undergraduate student with experience in programming; a computer scientist with an interest in biology and a biologist with an aptitude for computers [6; J.M.Williams et al
., personal experience]. By the mid 1990s formal bioinformatics classes were being designed and implemented at many universities and colleges. Today bioinformatics curricula are available from universities and colleges, many community colleges and even forward-thinking high schools, either online or on site [8–11
]. Therefore to obtain a degree and credentials in the field of bioinformatics, one only needs to search for, select, and enroll in a program that best suits one’s personal goals.
We will not be focusing on such ‘formal’ bioinformatics education in this review. Instead we will focus on less formal sources of bioinformatics education, which are available to biomedical scientists interested in managing and analyzing any manner of biological data. The review will be presented from the perspective of OpenHelix, a company focused on assisting a wide-range of interested persons to better utilize public bioinformatics resources. Through years of experience, the members of OpenHelix have gained a unique understanding for the needs of bench biologists as well as the value of bioinformatics databases, tools and other resources. We appreciate that in the life cycle of biologists, the need for up-to-date training spans the student, the scholar, the staff, the faculty and the administrators of programs. Lifelong learning is crucial for career development, and staff that are new to projects require training continuously. Ongoing learning opportunities outside of formal settings are required. Our efforts allow us to interact with these resources, their biocurators, and others in the arena of informal bioinformatics education. In this review we hope to share our knowledge of a variety of these informal bioinformatics educational opportunities so that a broad range of bioscientists may utilize these resources more easily.
In its infancy, the field of Bioinformatics was largely synonymous with the need to generate computer code in order to analyze biological information [12
]. As a result, bioinformatics education implied a mechanism by which one could learn computer languages and the principles or best practices for creating code that would generate statistically significant, rigorous analyses of biological data. This need to generate code has the ability to alienate some biologists who do not envision themselves as being ‘computer programmers’. At live trainings and conferences bench scientists still express hesitancy to venture into the realm of bioinformatics to members of OpenHelix, and they tell us that the level of bioinformatics and programming support varies enormously at their different institutions. As the field of bioinformatics has developed and matured, databases, tools and other bioinformatics resources have become available to scientists that allow data to be manipulated through the use of these resources without code being generated by individual users. Researchers in scientific disciplines as diverse as population genetics, epidemiology, disease research, structural biology and environmental biology are finding that they need an understanding of basic bioinformatics techniques and specific bioinformatics applications in order to analyze the vast amounts of data being generated in their field. As new technologies enable the generation of larger amounts of data, it is likely all scientists will need to utilize bioinformatics in some form or another. It will not be enough to be current in the literature in one’s field because ‘big data’ research projects already overwhelm the traditional publication methods [14–16
]. Only a fraction of the data from research consortia can be touched upon in their publications. Access to the rest of the data requires an understanding of the software resources, features and queries to make the data useful to biomedical researchers. For many bioscientists their bioinformatics requirements have shifted from a need to generate code to a need to understand the availability and functionality of public bioinformatics software, including databases, tools, algorithms and other resources, in order to mine, extract and effectively use the data within the resources [17–19
Figure 1: Although biological databases are only a fraction of all available bioinformatics software resources, their rise is representative of the overall growth of these resources, and is concurrent with the number of base pairs released in GenBank. This figure (more ...)
A new, less formal type of bioinformatics education is being developed for this type of need. It can be termed ‘outreach’, which is defined as ‘
the act of extending services, benefits, etc., to a wider section of the population, as in community work
]. An important mandate of bioinformatics education has become to extend the services and benefits from the field of bioinformatics to a broader audience of bioscientists who predominantly are not making full use of the available tools [21, 22; J.M.Williams et al
., personal communications].
To accomplish its outreach mandate, bioinformatics education needs to do a minimum of four things:
- raise awareness of the available resources
- enable researchers to find and evaluate resource functionality
- lower the barrier between awareness and use of a resource
- support the continuing educational needs of regular resource users
Ideally bioinformatics education will also be able to channel user feedback and suggestions back to the resource developers. This will ultimately improve existent resources by guiding the development of new features in existing tools as well as guiding the creation of new tools that possess features required by biomedical researchers. In this article we will discuss each of these aspects of informal bioinformatics education and review practical sources of each.