A New Online Computational Biology Curriculum

(http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003662)

Abstract

A recent proliferation of Massive Open Online Courses (MOOCs) and other web-based educational resources has greatly increased the potential for effective self-study in many fields.This article introduces a catalog(目录) of several hundred free video courses of potential interest to those wishing to expand their knowledge of bioinformatics and computational biology. The courses are organized into eleven subject areas modeled on university departments and are accompanied by commentary（注释，说明） and career advice.

Citation:Searls DB (2014) A New Online Computational Biology Curriculum. PLoS Comput Biol 10(6): e1003662. https://doi.org/10.1371/journal.pcbi.1003662

Editor:Francis Ouellette, Ontario Institute for Cancer Research, Canada

Published:June 12, 2014

Copyright:© 2014 David B. Searls. This is an open-access article distributed under the terms of theCreative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Funding:The author received no specific funding for this article.

Competing interests:The author has declared that no competing interests exist.

Less than two years ago, the author published an online bioinformatics curriculum in this journal and made the claim (with some important caveats(提醒) that a sufficient number and variety of free video courses had made their way to the web that it was possible to obtain a reasonably comprehensive bioinformatics education on one's laptop[1]. In that compilation(编辑) of courseware(课件), only a few entries（词目，条目） originated from the then-nascent（初期的) Coursera platform (https://www.coursera.org), and none came from its academic competitor edX (https://www.edx.org). In the intervening（干预，介入） time, these platforms and several others have fairly exploded(爆发) with new content, such that on the order of a thousand courses are now available online from over a hundred academic institutions. That fact alone justifies an update to the curriculum and a reassessment(重新评估) of the viability（生存能力，可行性） of online education in this field.

To begin with the latter, it should first be acknowledged that MOOCs are controversial（有争议的） in many regards. This article will not attempt to review or comment on the generic issues beyond making a few general observations in the Conclusion below. It is the opinion of the author that MOOCs are indeed a valuable resource even if they are not a magic bullet.The general limitations as regards bioinformatics were discussed in the previous article[1]and in a companion piece giving practical advice to online learners[2] and need not be recapitulated here. Certainly the sizeable increases in content that have occurred in the interim（过渡时期） have improved the prospects, yet they have also raised the bar, and it is now clearer than ever where the gaps and shortcomings are in the available curriculum. Specific instances will be commented upon in the appropriate（适当的，合适的） contexts below. One general observation is that the MOOC universe provides good coverage（覆盖） at the introductory level and plenty of specialized “elective” courses, but comprehensive intermediate（综合的，中间的） and advanced courses are thin on the ground in some areas, including biology. For example, as of this writing there are no MOOCs dedicated to the subject of structural biology, which is surprising given the importance of visualization（形象化） in the field and the availability （有效性）of excellent online resources. Nevertheless, the sizeable expansion of courses available, particularly in allied（联合） fields such as neurosciences and evolutionary biology, has been deemed（认为） sufficient（足够的） to widen the scope of this edition to encompass （包含）the more expansive term “computational biology” as opposed to “bioinformatics” (for those who consider the distinction（区别，差异） important).

MOOCs continue to generate large enrollments, at least initially（起初）, and these numbers together with anecdotal（轶事的） evidence from course discussion forums indicate active interest in online education among a certain population. This evidently extends to the readership of PLOS Computational Biology, judging from article-level metrics（度量） for the original curriculum[1], which has now attracted over 60,000 views and as of a year after its appearance was the 12th most viewed article in the history of the journal (per data available fromhttp://www.ploscompbiol.org/static/almInfo).

Those same metrics reveal high levels of interest in skills improvement and career advice, a conclusion that is based upon the popularity of the “Ten Simple Rules” series,which accounts for（对，，做解释） six of the ten most viewed articles. The topics of these six include giving talks[3], making posters [4], getting published [5], obtaining grants [6], selecting postdoctoral positions [7], and choosing between career paths in academia and industry [8] (the final article also having been written by this author). To better accommodate（调节，适应） these interests, the current edition of the curriculum has been extended in two ways. First, articles have been included (at the end of the catalog) that specifically address nonscientific skills likely to be useful in career development. Second, the commentaries（评注） on individual courses now include not only evaluations of their content but also career advice and other personal comments tied to that subject and based on the experiences of the author, both in the classroom (real and virtual) and over the course of a varied career in bioinformatics. These features are described in more detail below.

Conclusion

As noted in the Introduction, MOOCs are controversial in many regards and certainly not universally acclaimed. Many of the criticisms, however, have been or are being addressed to some degree. Identification verification technologies have lent more legitimacy（合理，合法） to assessment and certification. Particularly with courses that are well staffed with teaching assistants, the availability of individual attention can be surprisingly high, and often the discussion forums are a satisfactory substitute（代替） for direct student-teacher interaction. Curricula are becoming better coordinated by virtue of the release of entire packages of courses in a given area of study by a single institution, in what Coursera calls “Specializations” and edX calls “XSeries.” Increasingly imaginative approaches are being taken by individual courses to designing student activities so as to better simulate classroom, laboratory, or field experiences, though much remains to be done in this arena. Assessment, which remains very uneven in quality and effectiveness, may in fact not be much worse than in real courses and at least has the potential to benefit greatly from across-the-board quality-control measures, technology improvements, and data-mining approaches afforded by the nature of MOOCs.

What must be weighed against the hurdles（障碍） facing MOOCs and online learning is the tremendous variety and increasing depth of courses available. As can be seen in the catalog, there is often a choice among competing courses for popular topics, and while some more advanced subjects may not be offered exactly when they are wanted, sometimes the material is available offline, and there are enough courses that several of interest are almost certainly running at any given time. Having now taken comparable numbers of real and virtual courses, the author is firmly of the opinion that both types are normally distributed with regards to quality and that the distributions largely overlap. The subpar MOOCs can be sampled and discarded at very little cost, and the best MOOCs are very good indeed.