Lonnie Welch; Fran Lewitter; Russell Schwartz; Cath Brooksbank; Predrag Radivojac; Bruno Gaeta; Maria Victoria Schneider

“ Therefore, a bioinformatician must have the ability to apply software engineering methodologies to successfully design, implement, and maintain systems and software in scientific environments. The ability to employ modern software engineering processes (such as object-oriented analysis, design, and implementation) is important. In order to develop efficient and effective software systems, it is valuable to have a detailed understanding of the methods of algorithm design and analysis, machine learning, data mining, and relational databases. ”

“ Thus, a bioinformatics engineer must have strengths in computational and statistical sciences and must have general competency in biomedical sciences. Bioinformatics engineers design the infrastructure and systems for bioinformatics analysis, integrating software, databases, and hardware. This can involve the choice or design of hardware and software for the storage and management of diverse and distributed data, selection or development of tools and algorithms for integration and analysis of these data, and design of suitable user interfaces. ”

“ Not surprisingly, general skills needed at the PhD level include those skills necessary at the master level, as well as communications skills, management skills, and the ability to help others. Skills most frequently found lacking in individuals with PhDs include communications skills, ability to synthesize information, ability to complete projects, and leadership skills. The domain-specific skills were similar to those needed at the master level, but emphasized more prior experience in bioinformatics, data analysis, and statistics. ”

“ Additionally, a bioinformatician should be able to incorporate components from open source software repositories into a software system. The ability to effectively utilize distributed and high-performance computing to analyze large data sets is essential, as is knowledge of networking technology and internet protocols. A bioinformatician should be able to utilize web authoring tools, web-based user interface implementation technologies, and version control and build tools (e.g., subversion, Ant, and Netbeans) . ”

“ As the practices of genomic and personalized medicine increase, we anticipate a growing need for training clinicians in the use of bioinformatics data and tools. Other bioinformatics users include legal professionals and K-12 biology teachers.
The authors use personas to refine their understanding of different types of computational biologists and the competencies that they require to perform their roles. Designers of commercial products frequently create “personas”—archetypes based on data and research on the users for whom a product is being designed—to facilitate the design process. ”

“ As the discipline of bioinformatics and computational biology expands and matures, it is important to characterize the elements that contribute to the success of professionals in this field. These individuals work in a wide variety of settings, including bioinformatics core facilities, biological and medical research laboratories, software development organizations, pharmaceutical and instrument development companies, and institutions that provide education, service, and training. ”

“ At the bachelor level, managers are looking for people who can work independently, have good communications and consulting skills, are organized, and are passionate about their work. The most frequently mentioned domain-specific skills needed for bachelor-level candidates were technical in nature and included programming, software engineering, system administration, and databases. New hires for such positions at the bachelor level typically lack time management skills and project management skills and are unable to manage multiple projects. They also lack knowledge in biology and statistics. ”

“ The responses of the core facility directors can be summarized as follows: everyone wants smart, motivated people with good critical thinking skills and deep domain knowledge. It is clear that training in both general skills and domain-specific skills is necessary at all professional levels, both while in a degree program and throughout one's career. ”

“ The bioinformatics literature provides valuable perspectives on bioinformatics education by defining skill sets needed by bioinformaticians, presenting approaches for providing informatics training to biologists, and discussing the roles of bioinformatics core facilities in training and education. ”

“ With respect to domain-specific skills, directors need people well versed in biology, bioinformatics, statistics, and programming, essentially needing people with technical experience in both biological sciences and computational methods. New hires often lack experience in the analysis of real biological data. ”

“ While it is important for a bioinformatician to have a suite of computational, mathematical, and statistical skills, this alone is insufficient. Throughout their careers, bioinformaticians usually contribute to a variety of scientific projects, such as variant detection in human exome resequencing; human genetic diversity ”

“ The skill sets required for success in the field of bioinformatics are considered by several authors: Altman [2] defines five broad areas of competency and lists key technologies; Ranganathan [3] presents highlights from the Workshops on Education in Bioinformatics, discussing challenges and possible solutions; Yale's interdepartmental PhD program in computational biology and bioinformatics is described in [4] , which lists the general areas of knowledge of bioinformatics; in a related article, a graduate of Yale's PhD program reflects on the skills needed by a bioinformatician [5] ”

“ The columns of Table 2 indicate core competencies for three different types of individuals that have a need for bioinformatics training. (The three categories of bioinformatics training are not meant to capture all possible types of bioinformatics training needed but to describe three common categories.) Bioinformatics users access data resources to perform job duties in specific application domains. Bench-based researchers, both in academia and in industry, provide the classic example of a bioinformatics user, but this group is broadening in scope. ”

“ While we acknowledge that we are dealing with small samples of responses, not randomly surveyed, the resulting competencies do not contravene previously published recommendations (see introduction and references [1] – [16] ) , and they comport with the experiences of the task force members. The wording for the core competencies is modeled after the Accreditation Board for Engineering and Technology (ABET) criteria for computer science programs [18] , using the terminology and concepts of Bloom's Taxonomy [19] – [20] . ”

“ The task force hopes to have, in the future, a central system in which program officials can identify their programs and describe the coursework they require, yielding a database that can be mined to uncover common practices and variations across programs at multiple levels. Such a repository could be made available for public viewing, as we expect it will have incidental benefits for others, such as potential students looking to compare programs. ”

“ General skills needed include those that are more interpretative and problem solving, as well as personal traits, such as being independent, curious, and self-motivated. These same skills are considered lacking in many master-level hires. ”

“ Several approaches to providing bioinformatics training for biologists are described in the literature. Tan et al. [9] report on workshops conducted to identify a minimum skill set for biologists to be able to address the informatics challenges of the “-omics” era. ”

“ An ability to use current techniques, skills, and tools necessary for computing practice,” one should consider including adequate time for familiarization with the command line, data management practice, and statistical analysis tools.
File:Pcbi.1003496.g002A persona based on a typical “bioinformatics user.” QA: Quality Assurance, GUI: Graphical User Interface.Image credit: Jenny Cham, Mary Todd Bergman, and Cath Brooksbank, EMBL-EBI. Bioinformatics scientists are biologists who employ computational methods in order to advance the scientific understanding of living systems. ”