Training data for ChIP-seq data analysis (Galaxy Training Material): Identification of the binding sites of the Estrogen receptor

<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes ChIP-seq data from a study published by Ross-Inness et al., 2012 (DOI:10.1038/nature10730) to identify the binding sites of the Estrogen receptor, a transcription factor known to be associated with different types of breast cancer.</p

Training data for 'From peaks to gene' tutorial (Galaxy Training Material)

<p>The data provided here are part of a Galaxy Training Network tutorial that analyzes peaks from a study published by Li et al., 2012 (DOI:10.1016/j.stem.2012.04.023) to identify target genes</p

Recommendation starting points: Organizations and institutions—Top-down.

Recommendation starting points: Organizations and institutions—Top-down.</p

Full list of 14 recommendations.

A list of all recommendations developed and accepted by the authoring group. (DOCX)</p

The Bicycle Principles.

“The Principles” represent a framework for recommendations to improve SFT. One cycle comprises "Core Principles" that all SFT should meet, that is, SFT should be: (based on) Best Evidence, Effective, Inclusive, Catalytic. The second cycle of “Community Principles” apply when the SFT is developed with the potential or intention to be reused and disseminated beyond the original or initial deployment, that is, it should promote: Reach, Scale, and Sustain. These two iterative cycles make up the “bicycle”.</p

Complete example: Recommendation A.

Detailed example of a recommendation produced by the author group. (DOCX)</p

Differences and similarities between short-format training (SFT) and formal higher education (FHE).

SFT is highly variable: contrasting features of short-format training (SFT) and formal higher education (FHE). We wrap SFT with a dashed-line highlighting that any given SFT may be difficult to define exactly (see expanded definition of SFT, Supplemental Information, S1 Text); FHE’s solid line indicates its greater uniformity and lower variation. The Time of instruction in SFT is short—from hours to a few weeks—vs. many weeks for a course in FHE. The Format of SFT in the life sciences is typically focused on some form of active learning vs. more traditionally lecture-heavy FHE. Prerequisites are easier to define and enforce in FHE, unlike in SFT. Learner preparation is also difficult to predict in SFT, vs. FHE where learners will have been predictably prepared by prior coursework or the course is designed to be foundational. Instructors in SFT are often domain experts but may have limited teaching experience; FHE instructors will usually have some expectation of preparation for teaching, may have been teaching the material regularly, and often have the benefit of access to, or being expected to use, expert assistance in the planning and delivery of instruction. Regulations, policies, and laws usually apply to FHE courses; frequently, the informal nature of SFT is not affected by these and in practice SFT may not be regulated the same way as formal classroom instruction. Sequence of classes in a FHE curricular program provides learners with clear guidance on next steps, whereas SFT learners must direct their own learning; there may be additional SFT opportunities that can assist them in achieving their objectives, but this is not common. Economics of FHE assigns a concrete value to instruction; features of instruction, such as quality, can command a higher price; incentivizing maximized quality. Instructional effort is generally compensated. SFT instruction may be made available without cost to learners, but this may result in an underestimation of the value or quality of instruction; there may be no economic incentives for optimizing “free” instruction. Instruction delivery may rely on uncompensated volunteer labor. Variability is the summation of all these characteristics. The variability of SFT is high [18], two courses on a similar topic may differ widely; instructional practices and curricula may not be documented for reuse. In FHE, variability in these characteristics is much lower; comparisons can be made across programs, allowing equivalencies and credit exchanges across institutions and programs. It is possible to make formal comparisons between distinct FHE programs (e.g., [34]) within one country or university system. Transferring from one higher education institution to another involves a systematic assessment of equivalence of prior work (e.g., [35]; see also [36]). This figure emphasizes the fact that perhaps the only shared characteristic of these instructional forms is that formal knowledge about teaching and learning ought to apply to both; and that strategies for improving FHE STEMM education would likely not be transferable to SFT without significant modification.</p

An international consensus on effective, inclusive, and career-spanning short-format training in the life sciences and beyond

Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFT’s effectiveness and inclusiveness. Education researchers, students in SFT courses, and organizations have called for research and strategies that can strengthen SFT in terms of effectiveness, inclusiveness, and accessibility across multiple dimensions. This paper describes the project that resulted in a consensus set of 14 actionable recommendations to systematically strengthen SFT. A diverse international group of 30 experts in education, accessibility, and life sciences came together from 10 countries to develop recommendations that can help strengthen SFT globally. Participants, including representation from some of the largest life science training programs globally, assembled findings in the educational sciences and encompassed the experiences of several of the largest life science SFT programs. The 14 recommendations were derived through a Delphi method, where consensus was achieved in real time as the group completed a series of meetings and tasks designed to elicit specific recommendations. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned with a purpose-built framework—“The Bicycle Principles”—that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.</p

Recommendation starting points: Individual SFT instructors—Grass roots.

Recommendation starting points: Individual SFT instructors—Grass roots.</p

Abbreviations and definitions.

Science, technology, engineering, mathematics, and medicine (STEMM) fields change rapidly and are increasingly interdisciplinary. Commonly, STEMM practitioners use short-format training (SFT) such as workshops and short courses for upskilling and reskilling, but unaddressed challenges limit SFT’s effectiveness and inclusiveness. Education researchers, students in SFT courses, and organizations have called for research and strategies that can strengthen SFT in terms of effectiveness, inclusiveness, and accessibility across multiple dimensions. This paper describes the project that resulted in a consensus set of 14 actionable recommendations to systematically strengthen SFT. A diverse international group of 30 experts in education, accessibility, and life sciences came together from 10 countries to develop recommendations that can help strengthen SFT globally. Participants, including representation from some of the largest life science training programs globally, assembled findings in the educational sciences and encompassed the experiences of several of the largest life science SFT programs. The 14 recommendations were derived through a Delphi method, where consensus was achieved in real time as the group completed a series of meetings and tasks designed to elicit specific recommendations. Recommendations cover the breadth of SFT contexts and stakeholder groups and include actions for instructors (e.g., make equity and inclusion an ethical obligation), programs (e.g., centralize infrastructure for assessment and evaluation), as well as organizations and funders (e.g., professionalize training SFT instructors; deploy SFT to counter inequity). Recommendations are aligned with a purpose-built framework—“The Bicycle Principles”—that prioritizes evidenced-based teaching, inclusiveness, and equity, as well as the ability to scale, share, and sustain SFT. We also describe how the Bicycle Principles and recommendations are consistent with educational change theories and can overcome systemic barriers to delivering consistently effective, inclusive, and career-spanning SFT.</div