Trainer resources

GOBLET recommends developing a course with audience, objectives and outcomes in mind. Further, GOBLET recommends using competencies as a framework for course content development. Competencies can also be mapped to existing courses. Below are links to relevant guidelines documents as well as links to sites with training materials for courses.

Guidelines documents

1. Guidelines for developing and updating short courses and course programmes 
2. Book – Nicholls, Gill. Developing teaching and learning in higher education. Routledge, 2002.
3. Developing Training Material Guide (non-competency specific)

Core Competencies for Building Bioinformatics Courses

Using competencies as a framework for course content development can help ensure your content is relevant for the skills needed in the field. Below is a collection of bioinformatics competencies and how they can be used for building a course:

1. ISCB competencies V1, V2, V3 
2. ISCB competency progress reports: First Report, Second Report  
3. NIBLSE competencies – A publication to serve as a guide for institutions as they work to integrate bioinformatics into their life sciences curricula
4. BioExcel competencies mapped to courses: 
   1. View in BioExcel Knowledge Resource Center – 
   2. View in Competency Mapper – A web-based tool to support the creation and management of competency frameworks for professionals working in the biomolecular sciences
5. UK National Occupation Standard for Bioinformatics –  Drilled down for bioinformatics, the UK National Occupational Standards (NOS) are statements of the standards of performance individuals must achieve when carrying out functions in the workplace, together with specifications of the underpinning knowledge and understanding
6. UK Level 7 Apprenticeship standard for bioinformatics scientists (includes assessment endpoints)
7. CourseSource Bioinformatics Learning Framework – A publication describing a learning framework for a bioinformatics course that is part of the CourseSource initiative
8. Engineers Australia Stage 1 Competencies – Describes the expectation of the development of the engineer who on graduation satisfied the Stage 1 Competency Standard for Professional Engineer in Australia.
9. A clinical bioinformatics competency framework to support Health Education England to prepare clinical practitioners for the application of genomics in the healthcare service 
10. ISCB Education COSI Youtube collection, especially Youtube video – Implementing a competency-based training strategy for biomolecular researchers with high computational needs

Links to sites with Training Materials for courses

Knowing where to look for curated high-quality bioinformatics training materials can be difficult. We have compiled a list of trusted locations to visit when searching for materials, ideas and other educational resources for teaching on a variety of bioinformatics topics.

Repositories/Collections of Training Materials

1. GOBLET training portal – A collection of bioinformatics training materials including slide decks and exercises from leading bioinformatics education organizations around the world.
2. TeSS – Life sciences training resources, aggregated from ELIXIR nodes and 3rd-party providers
3. CourseSource – An open-access journal of peer-reviewed teaching resources for undergraduate biological sciences
4. The NIH Big Data to Knowledge (BD2K) Training Coordinating Center’s Educational Resource Discovery Index (ERuDite) framework. Search for resources here – ERuDIte is the educational resource discovery index that powers the BD2K Training Coordinating Center (TCC) Web Portal. 
5. BioExcel Knowledge Resource Centre – Bioinformatics training resources from the Centre of Excellence for Computational Biomolecular Research.
6. NIBLSE Learning Resource Collection – An effort to collect, customize, and disseminate high quality bioinformatics learning resources

Organization/Institution Specific Collection of Training Materials

1. UC Davis Bioinformatics Core training collection – Training workshop course materials from UC Davis Bioinformatics data analysis services and training program
2. Galaxy Training Resources / Network – A collection of tutorials developed and maintained by the worldwide Galaxy community
3. Bioinformatics.ca Canada – Course materials from the advanced bioinformatics workshops held by Bioinformatics.ca, including slide decks, exercises and data sets 
4. XSEDE Training portal – Training classes and materials to teach users how to maximize their productivity and learn new technologies for using XSEDE services
5. Cornell Virtual Workshops (HPC, programming) – Virtual programming and computing workshops offered by Cornell University
6. PRACE Best practices guide (HPC, MPI) – Best practice guides from the Partnership for Advanced Computing in Europe (PRACE)
7. Rosalind – A platform for learning bioinformatics and programming through problem solving
8. AWS Cloud computing training – Get hands-on practice in a live AWS environment with AWS services and real-world cloud scenarios. Follow step-by-step instructions to learn a service or practice a use case.
9. Google Cloud training labs – Online, self-paced labs give you hands-on practice with Google Cloud technologies in a live environment. Follow step by step instructions to master popular services and real-world use cases.
10. Critical Guides and Practical Guides in GOBLET Training Portal –  

F1000Research Bioinformatics Education & Training Collection – This collection is dedicated to publishing content (e.g., papers, slides, posters, reports or other documents) relating to bioinformatics and data science training and education

The Bioinformatics Training community has embraced the idea of ‘FAIR’ for training materials in order to widen their quality, accessibility and reach. Below we have linked to resources on metadata best practices to enable you to FAIRify your training materials.

1. Bioschemas related information:
   1. Bioschemas Training Specifications
   2. Bioschemas Training Portal
   3. Bioschemas Generator
2. ELIXIR FAIR Training Working Group
   1. Evaluate how FAIR your training resources are
   2. 10 recommendations to make your training materials FAIRer
3. Ontologies in the field
   1. EDAM Ontology browser for categorizing your training: 
   2. Educational Resource Discovery Index (ERuDIte)
      1. https://bioint.github.io/erudite-training-resource-standard/ 
      2. https://bigdatau.ini.usc.edu/assets/pdf/AmbiteEtAl-IEEE_ERuDIte_paper_2019.pdf 
      3. ERuDIte on FairSharing.org
4. How to build GitHub pages/wikis/websites for courses/training materials [COMING SOON]

Just as important as good training materials is a well organised training event. Below GOBLET has compiled a list of templates and best practices to help.

A training organiser/facilitator is responsible for the smooth running of a training event from conception to completion. Depending on the format and design of your training event, this may include, but is not limited to: programme development, budget organisation, travel logistics, marketing and advertising, applicant registration, venue booking and event management. Here is a collection of relevant templates to repurpose and use during workshop organisation:

1. Workshop schedule template
2. Workshop call template
3. Workshop timeline guidelines
4. Workshop logistics guidelines
5. Airline Booking template
6. Bid to Host a Workshop and Budget template
7. Applicant selection templates
   1. Defining selection criteria [COMING SOON]
   2. Example application form [COMING SOON]
   3. Example notification / invite letter
   4. Example registration award or travel award letter

1. Marketing & event management [COMING SOON]
   1. Course advertisement [COMING SOON]
   2. Badges / name-tags / tent cards
   3. Certificates of attendance / completion
   4. Participant biographies & faculty biographies
   5. Funder recognition and promotion in announcements [COMING SOON]
   6. Contact lists – useful list of relevant contacts for training (with GDPR / data protection compliance to share list)
   7. Photo consent

A code of conduct is a set of rules outlining the normal practices, responsibilities and expectations of course organisers, trainers and trainees. Ensuring that all parties have an understanding of the code of conduct allows the creation of an inclusive, safe and respectful learning environment for everybody.

1. Code of conduct examples
   1. ISCB Code of Conduct
   2. Bioinformatics.ca Code of Conduct
   3. EMBL Code of Conduct
2. Guidelines for facilitating a course [COMING SOON]

Just as important as good training materials is a well delivered training event. As a trainer, you are responsible for delivering the course. You are likely to have been involved in the programme development, decisions around workshop format as well as the creation of course materials. There are a range of workshop formats and teaching styles that have been successfully employed in a number of different environments. Below GOBLET has compiled a collection of relevant examples, templates and best practices to help you when preparing to deliver training:

1. Information about styles of classrooms
   1. Blended training model
   2. Project based learning 
   3. Online versus classroom learning
   4. Blended learning model → Combine with 1. 
   5. Computational biology flipped classroom
2. Best practices document
   1. SLING 
   2. Best practices in bioinformatics training for life sciences
   3. GOBLET bioinformatics training best practices workshop
   4. Techniques for facilitating in classroom engagement

1. Strategies for Group Discussion – 
2. Effective Group Discussion – 

1. Technologies for facilitating in the classroom
   1. Slack – is a communication and task management tool. It can be used in the classroom together with a learning management system to encourage communication between course participants. 
   2. An extensive list of technologies/software platforms to support virtual training environments and communication
2. Template for creating hands-on practicals including how to include code in your material

1. How to use the cloud, VMs and containers in bioinformatics training
   1. ELIXIR Workshop on how to use clouds and VMs in Bioinformatics 
   2. Slides from a workshop on using containers in training

ERuDIte Resources related to cloud training

Knowing how to appropriately assess trainees can be challenging. Resources below are intended to shed some light on this.

1. Assessment methods
   1. Overview of assessment methods
   2. Future learn: Assessment : What students think 
   3. Brown 1999 (book) Monitoring learner progress
   4. Using Bloom’s taxonomy to assess learning outcomes
   5. Self reflection / assessment form for trainers [COMING SOON]
2. Formal assessment
   1. Pre and post course assessment [COMING SOON]

UK Apprenticeship standards for Bioinformatics Scientist Degree with accompanying End-point Assessment Plan

Evaluating the quality and impact of a course can assist in improving and/or strengthening future training.

1. Minimum information standard:
   1. ELIXIR training quality and impact assessment strategy
   2. Inspiring Young People In STEM: Feedback Tools for STEM Ambassadors – Learn how to obtain and use feedback to help you improve your volunteering and STEM activities with young people 
2. How to gather training statistics, audience demographics, and quality of service metrics in the short term (i.e. administered directly after training):
   1. Recommend that you are consistent in the data elements that you collect for all of your training events / courses. This will help with enabling comparable evaluations of  different training courses /events and ease the review of training evaluation statistics reporting. 
   2. Consider what demographics or key information are needed to collect from trainees in order to produce training statistics and audience demographics
   3. It may be worthwhile extending evaluations of training against any other similar trainings a trainee may have attended
   4. How to avoid bias when evaluating training:
      1. Boring et al.
      2. 5 Elements to Include in any Post Training Evaluation
3. Training Impact in the long term (i.e. administered 6 months to 1 or 2 years after training, in 6 month intervals)
   1. 10 simple Rules for Measuring Impact of Workshops
   2. Continuing Education Workshops in BioInformatics Positively Impact Research and Careers
   3. Using core competencies to evaluate course impact [COMING SOON]
   4. When measuring long term training impact, how do you accommodate for external training impact [COMING SOON]
4. Handling data from assessment forms [COMING SOON]
   1. Classification
   2. How to handle comments/suggestions
   3. How to use feedback data to improve future iterations of a course/new course development

Endorsement is intended to provide a process by which one can have a well-established body like ISCB certify that the course meets the standards for an education program in the domain of computational biology and bioinformatics.

There are in general, 2 main types of COURSES that could be endorsed:

1. Bioinformatics short-course (TRAINING course of hours to one or two weeks in length)
2. Bioinformatics degree course (ACADEMIC course of two weeks to a term in length) 

WHY one want to endorse and affiliate a short-course: 

• Public and international recognition of the course as being evaluated and positively associated with the ISCB 
• Course providers gain additional exposure of their training to a highly relevant audience worldwide
• ISCB members gain access to a carefully selected catalogue of courses, and discounted rates to some courses
• ISCB is able to provide additional member benefits, making it more attractive to potential new members. This, in turn, benefits the broader computational biology community

WHY one want to endorse and accredit a degree course: 

• Public and international recognition of the course as being evaluated and positively associated with the ISCB 
• Course providers gain additional exposure of their training to a highly relevant audience worldwide
• ISCB student members can have a clear worldwide collection of educational institutions and universities that provide good quality courses on Bioinformatics

1. Guide for ISCB Endorsement & Affiliation of a short-course – [COMING SOON]
2. Guide for ISCB Endorsement & Accreditation of a degree course – Draft Template and Draft Process

When teaching bioinformatics at high school level, one should consider the curriculum and the language that is being used as this might be useful in deciding the content and level of standard.

1. Existing High School Teaching Materials
   1. GOBLET Practical Guides
      1. Bioinformatics – the Power of Computers in Biology: A Practical Guide
      2. Using Bioinformatics to Understand Genetic Diseases: A Practical Guide
   2. mGen – An online and mobile app for promoting engagement between high school learners and research staff
   3. SEA-PHAGES Bioinformatics Guide – An online Bioinformatics guide to turn a new phage genome sequence into a refined annotation
   4. European Learning Laboratory for the Life Sciences (ELLLS) – Resources for teachers and students
      1. ELLLS TeachingBase – A collection of molecular biology teaching modules designed for teachers and students
      2. The NODE – a community site for and by developmental biologists
   5. TReND – scientific training using low-cost open source tools and model systems for scientific research
   6. ISCB Collection of Bioinformatics Resources for High School – a collection of resources from the International Society for Computational Biology
   7. NAVIGENE – a tool to navigate through bioinformatics. You can use it in class to design lessons on genomics, genes and proteins.
   8. GenSCOP genetics app – a student led project from the Sydney Brenner Institute for Molecular Bioscience (SBIMB). The app is designed as a library containing simple explanations of genetic concepts.
   9. Bioinformatics: Coding for Medicine – See how the worlds of computer scientists and medical doctors are merging together through a set of courses that give young students the right skills to contribute to this fast-changing scientific world.
   10. Whitehead, Bioinformatics and Research Computing (BaRC) – A collection for learning about bioinformatics and computational tools
   11. Teaching – Student projects – Bornberglab – Bioinformatics at the IEB 
   12. Didactic research in High School for innovative STEM bioinformatics – 
   13. Bioinformatics@school – Netherlands Bioinformatics Centre (NBIC) bring bioinformatics to the classroom with free online educational modules and information on bioinformatics
   14. How to design an anti-inflammatory drug without side effects for the stomach? – Interesting high school student bioinformatics activity
   15. 4273π – A freely available, customized distribution of Raspbian GNU/Linux for the Raspberry Pi computer. 4273π is for those wishing to teach, learn or use bioinformatics on the Raspberry Pi.

1. Relevant papers and materials on bioinformatics in the high school classroom
   1. Integrating bioinformatics into senior high school: design principles and implications – Here the authors present design principles of bioinformatics learning environments for high schools, and an integrated tool they developed which uses authentic inquiry based learning activities. 
   2. Bioinformatics in High School Biology Curricula – This study evaluates the representation of bioinformatics related content in secondary school science standards in 40 US states and district of Columbia (2007) 
   3. Bioinformatics Education in High School: Implications for Promoting Science, Technology, Engineering, and Mathematics Careers – This paper (2017) investigates the effects of a specific Bio-ITEST teacher professional development programme and bioinformatics curricula on awareness, engagement, self-efficacy and relevance in high school teachers and students to boost the interest in STEM careers. 
   4. Explaining Genomics and Bioinformatics to High School Biology Students – Describes an inquiry based learning activity for high school students, that also includes a short history of genomics and bioinformatics and their main applications as well as the relevancy to students’ lives. 
   5. Teaching Bioinformatics at the Secondary School Level – Experienced high school science teachers give ten tips on how to incorporate bioinformatics in science curricula. 
   6. Teaching High-School Biology: Materials and Strategies – Overview on how the high school biology programs at the precollege level should be adapted to meet the aspirational needs and projections for the future of youth in a changing society.
   7. Ten Simple Rules for Teaching Bioinformatics at the High School Level – Experience of a high school science teacher on how to incorporate bioinformatics in high school classrooms given the number of topics and tools allowing interactive instruction.
   8. Bringing Bioinformatics into the Biology Classroom – Slides from the SIB (Swiss Institute of Bioinformatics) introducing how bioinformatics basic resources can handle disease-related questions
   9. Kids.Net.Au – Encyclopedia > Bioinformatics – An introduction to Bioinformatics and examples of its most widely used applications
   10. Bioinformatics for middle school aged children – Enhancing teacher knowledge and confidence to integrate innovative instructional materials into K-8 classrooms and contributes to capacity building in STEM instruction
   11. Academic Kids – Bioinformatics – The major research areas related to Bioinformatics are presented, including associated software tools and very useful links.
   12. RRI-tools for Responsible Research and Innovation (many useful links included) – A reflection on how innovative pedagogical methods in STEM teaching can help introduce RRI principles in schools to foster STEM careers attractiveness. 

Science education policies in the European Commission: towards responsible citizenship – With the priority given to connect science to society under the EU projects umbrella, this article presents key aspects and objectives of “responsible” science education in Europe.

1. Big Data Biomedicine and Education – rationale for doing bioinformatics training
2. Envisioning the Future of ‘Big Data’ Biomedicine – The National Institute of Health (NIH) ‘Big Data to Knowledge’ programme (BD2K) 
3. Selection of the 10 rules papers
4. Report on surveys about bioinformatics training needs
   1. A Global Perspective on Evolving Bioinformatics and Data Science Training Needs (2019) 
   2. Unmet Needs for Analyzing Biological Big Data: A Survey of 704 NSF Principal Investigators (2016)
   3. Survey of bioinformatics and computational needs in Australia 2016
5. International training partnerships – An International collaboration between BD2K’s TCC, ELIXIR’s TeSS, bioCADDIE, GOBLET, EMBL-ABR and H3ABioNet to promote biomedical data science. 
6. Forums / networks for training discussion
   1. GOBLET – The Global Organisation of Bioinformatics Learning, Education and Training
   2. LifeSciTrainingSlack 
7. A good Example of a Biomedical Data Science Webinar Series

If you are looking for a resource that you cannot find here, or if you would like to suggest a resource, please contact us at info@mygoblet.org 

The GOBLET Trainer Resource Portal has been pulled together over time by the following individuals:

Education Summit, Capetown 2019

• Kim Gurwitz, University of Cambridge
• Michelle Brazas, Ontario Institute for Cancer Research
• Annette McGrath, CSIRO
• Sarah Morgan, EBI
• Victoria Nembaware
• Peter van Huesden
• Lyndon Zass
• Caleb Kipkurui
• Faisal Fadlemola
• Rolanda Julius
• Mamana Mbiyavanga
• Cath Brooksbank, EBI
• Judit Kumuthini
• Vera Matser
• Jasper van Horn
• Ben Moore, EMBL-EBI

Education Summit, Hinxton 2020

• Michelle Brazas, Ontario Institute for Cancer Research
• Ben Moore, EMBL-EBI
• Annette McGrath, CSIRO
• Maria Bernardi, EBI
• Dusanka Nikolic, WGC Advanced Courses, Hinxton Cambridge 
• Fatma Guerfali
• Javier De Las Riva
• Paballo Abel Chauke
• Sarah Morgan, EBI
• Nicky Mulder
• Shaun Aron, University of the Witwatersrand, Johannesburg, South Africa