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      A Report of the Curriculum Task Force of the ISCB Education Committee

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          Abstract

          Introduction The International Society for Computational Biology (ISCB) Education Committee (EduComm) promotes worldwide education and training in computational biology and bioinformatics and serves as a resource and advisor to organizations interested in developing educational programs. The topic of curricula for bioinformatics programs has long been of interest to ISCB and EduComm. Dr. Russ Altman, a founding board member and past president of ISCB, has been associated with one of the first bioinformatics degree programs (at Stanford University) and wrote an article on this topic [1]. Dr. Shoba Ranganathan, as chair of EduComm a decade ago, began organizing a yearly Workshop on Education in Bioinformatics (WEB) at Intelligent Systems for Molecular Biology (ISMB) meetings that generated exchange of information and many productive discussions. Curriculum development was one aspect of bioinformatics education covered in these sessions [2]. The field of bioinformatics has grown in the past decade. There are many such degree granting programs around the world at the bachelor's, master's, and PhD levels. This article provides a status report of the EduComm's ongoing endeavor to identify a set of core curricular guidelines for bioinformatics education at all levels. As a pilot project, the Curriculum Task Force of the EduComm conducted a survey in the spring of 2011. This initial survey was sent to members of the EduComm, consisting of 50 individuals from various regions of the world, and to the EMBnet community, representing 79 people from more than 30 countries. The response rate was 33%, with 41 individuals completing the survey. Analysis of the survey produced an initial set of recommendations to be used as a discussion point from which to launch a larger effort to develop a working bioinformatics curriculum. With increased input from the larger community, the EduComm will continue to refine its results. Individuals who are interested in contributing to this initiative are encouraged to contact the Chairs of the ISCB EduComm. The purposes of this article are to further disseminate the survey results and to solicit participation in the initiative. The initial survey results are summarized, the preliminary working curriculum is defined, and the next steps of the EduComm Curriculum Task Force are outlined. Survey Results Responses were received from 41 individuals in 20 countries (covering five continents). This is a small but diverse group of respondents representing a wide array of professional positions, including scientist, professor (all ranks), director of bioinformatics, technician, engineer, postdoctoral researcher, teaching assistant, and lecturer. The levels of students taught by the respondents ranged from secondary thru PhD. Topics suggested by survey respondents for inclusion in a bioinformatics curriculum fit into two primary areas, (1) computation, mathematics, and statistics and (2) biology and chemistry. An initial working bioinformatics curriculum was constructed by selecting topics suggested by at least ten respondents (i.e., more than 25% of the survey respondents), resulting in five topics in each of the two primary areas. This initial working curriculum is shown in Table 1. 10.1371/journal.pcbi.1002570.t001 Table 1 The initial working bioinformatics curriculum. Computation, Mathematics, and Statistics Biology and Chemistry Programming/scripting/software engineering (36) Cellular and molecular biology (21) Statistics/probability (31) Genomics (12) Databases (24) Basic biology (11) Algorithm design/data structures/computation theory (20) Evolutionary biology (10) Machine learning (13) Genetics (10) Each number in parentheses indicates the total number of survey respondents who recommend the corresponding topic. Analysis and Next Steps The results of our survey were presented at the Third RECOMB Satellite Conference on Bioinformatics Education (RECOMB-BE) [3]. Several observations and suggestions were offered during the discussion that followed the presentation. It was noted that the survey did not provide a list of possible topics from which to choose. This was intentional, to avoid introducing biases that would affect the answers. The unrestricted nature of the questions resulted in a wide array of topics being suggested. Responses that addressed similar concepts were grouped together to identify general topics. The initial working curriculum does not completely represent the breadth of suggested topics. For example, it does not contain anything explicitly related to medicine, structural biology, or biochemistry. A small minority of the respondents suggested these topics; thus, they are not reflected in the consensus. (Additional grouping could be performed in order to increase the coverage of the responses.) In addition, due to the diversity of suggestions, the topic categories above tend to be general areas rather than contents of specific courses. Furthermore, due to the use of the word topic in the survey, respondents suggested only content areas, not issues of process, which appear frequently in descriptions of desired program outcomes. Specific examples of missing items include (1) scientific communication, (2) lifelong learning, and (3) professional behavior (including ethics). It was also suggested that ISMB's topic areas be considered as a general framework for a bioinformatics curriculum. The most recent ISMB topic areas are as follows: Applied Bioinformatics Bioimaging & Data Visualization Databases & Ontologies Disease Models & Epidemiology Evolution & Comparative Genomics Gene Regulation & Transcriptomics Mass Spectrometry & Proteomics Population Genomics Protein Interactions & Molecular Networks Protein Structure & Function Sequence Analysis Text Mining This initial working curriculum is only intended to prompt discussion and to inspire the generation of more specific recommendations for refined curricula for bioinformatics. It provides useful guidelines for those seeking to determine core topics for a bioinformatics program (it is not intended to be used as a standard for accreditation purposes). The EduComm is currently (a) summarizing curricula from existing bioinformatics programs, (b) surveying directors of bioinformatics core facilities and biological researchers to identify the skills needed for people they hire, and (c) reviewing bioinformatics career opportunities to determine skill sets required by current employers of bioinformaticians. The new survey results may be used to propose curricular guidelines. The ISCB EduComm (http://www.iscb.org/iscb-leadership-a-staff-/1172) invites participation from the worldwide community of computational biologists and bioinformaticians. Please join us for the Birds of a Feather (BoF) session, entitled Curriculum Guidelines for Bioinformatics and Computational Biology (An Open Forum of the Curriculum Task Force of the ISCB Education Committee), which will be held on July 16, 2012 at the ISMB meeting (http://www.iscb.org/ismb2012-program/birds-of-a-feather). At the BoF session, the Curriculum Task Force of the ISCB Education Committee will hold an open forum to discuss bioinformatics curriculum guidelines. Participants will consider curricular implications of the task force's surveys of career opportunities, hiring practices of bioinformatics core facility directors, and existing curricula. The forum seeks input from all interested individuals. Additionally, we are seeking input via a blog. To read a more detailed report of the survey and to post your comments, please visit the blog site at http://bioinfocurriculum.blogspot.com/.

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          Bioinformatics Education—Perspectives and Challenges

          Education in bioinformatics has undergone a sea change, from informal workshops and training courses to structured certificate, diploma, and degree programs—spanning casual self-enriching courses all the way to doctorate programs. The evolution of curriculum, instructional methodologies, and initiatives supporting the dissemination of bioinformatics is presented here. Building on the early applications of informatics (computer science) to the field of biology, bioinformatics research entails input from the diverse disciplines of mathematics and statistics, physics and chemistry, and medicine and pharmacology. Providing education in bioinformatics is challenging from this multidisciplinary perspective, and represents short- and long-term efforts directed at casual and dedicated learners in academic and industrial environments. This is an NP-hard problem. Training in bioinformatics remains the oldest and most important rapid induction approach to learning bioinformatics skills. Both formal (short-term courses) and informal training (on-demand “how-to” procedures) have remained the mainstay of on-the-job programs. After almost a decade of short-term training, and retraining students, faculty, and scientists in discrete aspects of bioinformatics, the impetus to formalize bioinformatics education came in 1998 from Russ Altman [1], with a wish list of topics for an ideal bioinformatics educational program at the masters and PhD levels. Given the multidisciplinary nature of bioinformatics and the need for designing cross-faculty courses, by 2001 only a handful of universities had successfully commenced formal education in bioinformatics, with others waiting and watching. The Workshop on Education in Bioinformatics (WEB) 2001 (http://surya.bic.nus.edu.sg/web01/) was launched at the 2001 International Conference on Intelligent Systems for Molecular Biology (ISMB) as a satellite meeting, to provide for the first time a forum for bioinformatics educators to meet, discuss, and exchange ideas and suggestions. WEB addresses fundamental educational and pedagogical issues to determine the nature, extent, and content of, and delivery tools available for, bioinformatics degree and training programs, and to provide focus points and suggestions for improvement of nascent degree programs. WEB has served as the single annual meeting for education in bioinformatics, with plenary, oral, and poster presentations. WEB has, over the past four years, witnessed the evolution of bioinformatics education through talks and posters. Typically, presentations have sequentially progressed from a masters degree to a PhD [2,3] or from a minor to a complete program [4]. Several WEB attendees themselves started educational programs [5] and are now active members of the ISCB Education Committee, where a list of currently available educational programs is maintained [6]. The new educational initiatives showcased include the S* Life Science Informatics Alliance in WEB 2001 and the Worldwide Universities Network in WEB 2002. Special sessions on industry needs (WEB 2002) and pedagogy (WEB 2003 and WEB 2004) have also been included in the program to provide perspective and depth. Bioinformatics education became mainstream with the ISMB 2005 conference, featuring a joint education workshop integrating WEB with the efforts of the ISCB's Education Committee (referred to as WEB 2005 here) on the opening day of the conference. How well do the new graduates from these educational programs fit the jobs available to them? How many areas should a bioinformatics graduate be an expert in? Apart from a deep understanding of algorithms, programming, and life sciences, solving problems in genomics, proteomics, and/or medical informatics appears to be the current requirement. With the blurring boundaries between bioinformatics and new areas of endeavor such as forensics and biodiversity/ecoinformatics, where should we, as educators, draw the line? With industry's annual fluctuating demands for specific in-depth knowledge, how can we create a bioinformatics world? Some of these issues will be discussed in the 2006 WEB meeting. But here are four take home messages from the earlier workshops. First, with the growing demand for computational biologists, there is a persistent and continuing demand for bioinformatics education at all levels—formal and informal, face-to-face and distance learning, and short-term training and rigorous long-term academic programs. Clearly, “one size does not fit all” [7], since the trend is to develop new and innovative educational programs addressing niche areas within bioinformatics. Second, there is still no single bioinformatics education program that can satisfy today's wish list of essential ingredients [8,9]. But by enabling the student cohort in self-learning, with a problem-based approach [10], the ontology of education (“to draw forth”) is realized. Third, percolation of basic bioinformatics down to the undergraduate level, especially for all life science majors [11] and optionally for physical and computer science majors [12] would develop the multidisciplinary skills required for bioinformatics. Fourth, “faster, further, and more” summarizes the components that would go into curricula of the future. ISCB members, educators, and bioinformatics professionals are encouraged to participate in WEB, and contribute their valuable ideas and expertise to this bioinformatics educational initiative. 
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            A curriculum for bioinformatics: the time is ripe.

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              Author and article information

              Contributors
              Role: Editor
              Journal
              PLoS Comput Biol
              PLoS Comput. Biol
              plos
              ploscomp
              PLoS Computational Biology
              Public Library of Science (San Francisco, USA )
              1553-734X
              1553-7358
              June 2012
              June 2012
              28 June 2012
              : 8
              : 6
              Affiliations
              [1 ]School of Electrical Engineering and Computer Science, Ohio University, Athens, Ohio, United States of America
              [2 ]Department of Biological Sciences and Lane Center for Computational Biology, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
              [3 ]Bioinformatics and Research Computing, Whitehead Institute, Cambridge, Massachusetts, United States of America
              University of California San Diego, United States of America
              Author notes
              Article
              PCOMPBIOL-D-12-00705
              10.1371/journal.pcbi.1002570
              3386154
              22761560
              9edd8824-2548-4b0c-9820-bc2015df1610
              Welch et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
              Page count
              Pages: 2
              Categories
              Message from ISCB
              Social and Behavioral Sciences
              Science Education

              Quantitative & Systems biology

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