|Category 'D'- Education'|
|Poster - D01|
|The Regional Student Group program of the ISCB Student Council: stories from the road
|Magali Michaut, Netherlands Cancer Institute, Netherlands|
|Geoff Macintyre (NICTA Victoria Research Laboratory and The University of Melbourne, Diagnostic Genomics Australia); Thomas Abeel (Broad Institute of MIT and Harvard, Genome Sequencing and Analysis Program United States);|
|Short Abstract: Since 2006, the Student Council of the International Society for Computational Biology (ISCB) has run a Regional Student program where they affiliate with local student groups to lend them support. The experiences of this program are currently being discussed in a series of articles.
Each of these articles discusses various characteristics of students organisations in the fields of bioinformatics and computational biology. Local student groups outside the scope of University education are useful to develop dynamic communities and complement classical education. To support the discussion, we use real-life stories from the numerous Regional Student Groups (RSGs) established all over the world by the ISCB Student Council.
The ISCB Student Council has been running events and programs since 2004 in order to promote the development of the next generation of computational biologists. However, the overall student population shows very heterogeneous needs. Consequently, the RSG program was launched in 2006 in order to tailor the initiatives to the needs of students of various geographical regions. Based on all events and activities organised by the RSGs, we highlight here the emerging themes of such initiatives: Developing your career, Scientific meetings, Interactive science, Running an RSG: the challenges and benefits.
The goal of this series is to share our perspective and experience on these topics and hopefully inspire others to start similar initiatives in other regions or scientific communities.
|Poster - D02|
|Knowledge Exchange starts early: a year in industry scheme.
|Rubina Kalra, The Genome Analysis Centre, United Kingdom
|Vicky Schneider-Gricar (The Genome Analysis Centre) Vicky Schneider-Gricar (The Genome Analysis Centre, Training & Outreach United Kingdom);|
|Short Abstract: Exposure of undergraduates to different working research environmentsrepresents an excellent opportunity to form and provide a pragmatic opportunity for the students as well as the hosts to access their interaction and consolidate this with potential PhD opportunities. The Genome Analysis Centre runs a “Year in Industry scheme” which comprises 12 months training placements for undergraduate students during the third year of their degree (Biology, Biochemistry, Natural Sciences or Computer Science with an interest in Computational Biology).
These placements represent an invaluable opportunity to gain first-hand experience of a research environment, contributing to current research at the institute, whilst developing transferrable skills such as team work and time management. In this poster we present the structure, core elements, monitoring mechanisms we have developed, including the feedback collected from the first placements. Hear first hand the students perspectives on such placement here: http://www.youtube.com/watch?v=rW2vtvmE_7k
|Poster - D03|
|ChromosomeWalk, a virtual exhibition introducing the human genome and bioinformatics
|Marie-Claude Blatter, SIB Swiss Institute of Bioinformatics, Switzerland|
|Vivienne Baillie Gerritsen (SIB Swiss Institute of Bioinformatics, Swiss-Prot Group Switzerland); Patricia Palagi (SIB Swiss Institute of Bioinformatics, Proteome Informatics and Evolutionary Bioinformatics Groups Switzerland); Lydie Bougueleret (SIB Swiss Institute of Bioinformatics, Swiss-Prot Group Switzerland); Frederique Lisacek (SIB Swiss Institute of Bioinformatics, Proteome Informatics Group Switzerland); Marc Robinson-Rechavi (SIB Swiss Institute of Bioinformatics, Evolutionary Bioinformatics Group Switzerland); Ioannis Xenarios (SIB Swiss Institute of Bioinformatics, Swiss-Prot and VitalIt Groups Switzerland);|
|Short Abstract: ChromosomeWalk.ch is a virtual exhibition which explains the role of bioinformatics in the life sciences today.
The site offers scientific content that is varied and as comprehensive as possible. The graphic and web design were given great thought and have just been awarded two international prizes. Visitors are introduced to the world of DNA, proteins and bioinformatics by going on an interactive and recreational journey into the heart of human chromosomes. Starting at the level of a cell's nucleus, visitors discover each chromosome and the genes they carry. Answers are given to questions such as 'what is the human genome?', 'how do you design drugs?', 'who are our ancestors?' And a number of other options are offered: quizzes, a glossary, videos, links to bioinformatics resources (DNA sequences, 3D data, …), scientific publications and numerous popular science articles.
The site is PC, Mac and touchpad compatible. The web-based nature of the exhibition helps to reach a maximum number of visitors. Updates are also an easy task thus helping to sustain a long-term endeavour.
ChromosomeWalk.ch is currently both in French and in English. A German version will be available by the opening of ISCB 2013. The exhibition has been shown in Science Fairs and high school classes, and was greatly appreciated. Our poster highlights the different educational approaches used in ChromosomeWalk.ch.
|Poster - D04|
|Online Learning in Bioinformatics Continuing Education: Perspective from bioinformatics.ca
|Michelle Brazas, Ontario Institute for Cancer Research, Canada|
|Francis Ouellette (Ontario Institute for Cancer Research, Informatics and Bio-computing Canada);|
|Short Abstract: Classroom-based continuing education programs in bioinformatics have had to adapt to the introduction of videos channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool. Yet face-to-face instruction particularly in advanced topics in bioinformatics still plays a valuable role in the learning continuum. The model used by bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, blends more traditional classroom-based learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years, including moving from 2-week long general overview workshops to 2-day advanced topic-focused workshops, classroom feedback from across our different teaching models and our strategies for evaluating and introducing new learning tools that acknowledge and take advantage of the current online learning environment. We conclude with a look towards what the future holds for bioinformatics continuing education programs.|
|Poster - D05|
|Internship program for developing nations – an education initiative of the ISCB Student Council
|Geoff Macintyre, University of Melbourne, Brazil
|Mainá Bitar (Universidade Federal de Minas Gerais) Priscila Grynberg (Universidade Federal de Minas Gerais, Biochemistry and Immunology Brazil); Anupama Jigisha (University of Geneva, Swiss Institute of Bioinformatics Switzerland); Venkata Satagopam (University of Luxembourg, LCSB Luxembourg); Surya Saha (Cornell University, Department of Plant Pathology and Plant-Microbe Biology United States); Avinash Shanmugam (University of Michigan, Department of Computational Medicine and Bioinformatics United States); Mainá Bitar (Universidade Federal de Minas Gerais, Biochemistry and Immunology Brazil); Margherita Francescatto (German Center for Neurodegenerative Diseases, Genome Biology of Neurodegenerative Diseases Germany);|
|Short Abstract: Internships are a great way to supplement formal education by providing students with hands-on experience in the workplace. While commonplace and competitive in the developed world, students from developing nations have significantly fewer opportunities to access internship programs. However, it is precisely these students who can benefit most from an internship program, taking back a wealth of experience and ideas to their home nation.
In order to provide students in computational biology from developing nations with increased internship opportunities, the ISCB Student Council created a Developing Nations Internship Program. The program works as follows: Principal Investigators (PI) who choose to offer their open internship position to a developing nation student engage the ISCB Student Council to help. The Student Council uses their extensive Regional Student Group program to advertise the internship to students in developing nations. Relying on the vast Student Council volunteer network, internship applications are screened and shortlisted by the Student Council. The top three candidates are then provided to the Principal Investigator. This not only streamlines the process for PIs, but results in increased opportunities for developing nation students.
Since 2009, the program has filled seven internship positions, supporting students from Brazil (3), Kenya (1), India (1), Turkey (1) and Estonia (1) to be placed in research groups from Europe (5), United States (1) and Australia (1). This poster highlights the benefits of the program through detailed testimonies from past students and principal investigators.
|Poster - D06|
|Bioinformatics and Systems Biology: bridging the gap between heterogeneous student backgrounds
|Anton Feenstra, VU University Amsterdam & NBIC Netherlands Bioinformatics Centre, Netherlands|
|Sanne Abeln (VU University Amsterdam & NBIC Netherlands Bioinformatics Centre, IBIVU Centre for Integrative Bioinformatics & AIMSS Amsterdam Institute for Molecules Medicines and Systems Netherlands); Douwe Molenaar (VU University Amsterdam, IBIVU Centre for Integrative Bioinformatics & AIMSS Amsterdam Institute for Molecules Medicines and Systems Netherlands); Huub Hoefsloot (University of Amsterdam, SILS Swammerdam Institute for Life Sciences Netherlands); Bas Teusink (VU University Amsterdam & NBIC Netherlands Bioinformatics Centre, IBIVU Centre for Integrative Bioinformatics & AIMSS Amsterdam Institute for Molecules Medicines and Systems Netherlands); Jaap Heringa (VU University Amsterdam & NBIC Netherlands Bioinformatics Centre, IBIVU Centre for Integrative Bioinformatics & AIMSS Amsterdam Institute for Molecules Medicines and Systems Netherlands);|
|Short Abstract: Teaching students with very diverse backgrounds can be extremely challenging. This paper uses the Bioinformatics and Systems Biology MSc in Amsterdam as a case study to describe how the knowledge gap for students with heterogeneous backgrounds can be bridged.
We show that a mix in backgrounds can be turned into an advantage by creating a stimulating learning environment for the students. In the MSc Programme conversion classes help to bridge differences between students, by mending initial knowledge and skill gaps. Mixing students from different backgrounds in a group to solve a complex task, creates an opportunity for the students to reflect on their own abilities. We explain how a truly interdisciplinary approach to teaching helps students of all backgrounds to achieve the MSc end terms. Moreover, transferable skills obtained by the students in such a mixed study environment are invaluable for their later careers.
|Poster - D07|
|Teaching Computational Approaches for Life Scientists
|Amir Rubinstein, Tel Aviv University, Israel|
|Benny Chor (Tel Aviv University, Computer Science Israel);|
|Short Abstract: In recent years we witness many educational initiatives aiming to bridge the gap between the biological and the computational sciences. These include academic courses, bioinformatics boot camps, web-tools, etc. Among such initiatives, those aimed for life-science audiences usually focus on either teaching programming skills, or tool handling skills.
We design a new course – "Computational Approaches for Life Scientists", which aims to promote the computational "way of thinking", beyond the level of programming and tool handling. The course is a non-introductory course designed specifically for life scientists. It is taught in a less technical manner than in "pure" computer science courses, and avoids unnecessary formalism. It assumes prior basic programming skills (e.g. from high school). The focus is on abstract thinking, fundamental computing concepts and ideas, and basic computational approaches to biological problem solving. An additional goal is to expose students to discrete mathematics notions, a branch of mathematics underrepresented in life-sciences curricula.
At the first 2-3 weeks students are acquainted with the programming language Python, later used for demonstrating course topics and for developing hands-on skills. Python is both simple and expressive, and enables a rapid integration by students. Course topics include biological image processing, network notions and algorithms, basic sequence analysis concepts, discrete approaches to simulation of dynamic biological systems, and more.
This course is taught for the first time in 2013 at the Faculty of Biology, Technion, Israel. Both undergraduates and graduates are enrolled. The poster will present the course in more depth, and preliminary educational evaluation.
|Poster - D08|
|EMTRAIN: the European Medicines Research Training Network
|Catherine Brooksbank, EMBL-European Bioinformatics Institute, United Kingdom|
|Claire Johnson (EMBL-European Bioinformatics Institute, Training Team United Kingdom); Antony Payton (University of Manchester, Institute of Population Health United Kingdom); Anita Aperia (Karolinska Institutet , Department of Women´s and Children´s Health Sweden); Christa Janko (Medizinische Universität Wien, Department of Clinical Pharmacology Austria); Mike Hardman (Astra Zeneca, Science Policy and Relations United Kingdom);|
|Short Abstract: A plethora of training opportunities is available to postgraduates in the biomedical sciences, but finding the most appropriate training is challenging. EMTRAIN (www.emtrain.eu) is establishing a sustainable, pan-European platform for education and training, covering the whole life cycle of medicines research, from basic science through clinical development and pharmacovigilance.
EMTRAIN has three streams. Firstly, on-course® (www.on-course.eu) is a comprehensive online catalogue of postgraduate courses in the biomedical and medicines research and development fields relevant to medicines research and development, with quality indicators built in. It covers short courses, master’s courses and PhD programmes. Ultimately it will also have a section on learning methodologies and tools aimed primarily at course developers and we invite input to the functionality of this resource. Secondly, LifeTrain is working towards a mutually recognised framework for continuing professional development in the biomedical sciences. We are working with course providers (representatives from the ESFRI-BMS research infrastructures are an important representative group), professional bodies, employers and others to agree on a set of principles that will enable course seekers to find high quality training, course providers to gain meaningful recognition for developing training that meets LifeTrain’s quality standards, and employers to find and develop staff with appropriate and cutting-edge skills. Thirdly, a programme for public–private partnership PhD students intends to develop the next generation of industrially aware scientists.
EMTRAIN is supported through the Innovative Medicines Initiative, Europe’s largest public–private initiative, which aims to speed up the development of better and safer medicines for patients.
|Poster - D09|
|Training in tools and resources - the EMBL-European Bioinformatics Institute experience
|Sarah Morgan, EMBL-European Bioinformatics Institute, United Kingdom|
|Tom Hancocks (EMBL-European Bioinformatics Institute, Training Team United Kingdom); Laura Emery (EMBL-European Bioinformatics Institute, Training Team United Kingdom); Mindi Sehra (EMBL-European Bioinformatics Institute, Training Team United Kingdom); Cath Brooksbank (EMBL-European Bioinformatics Institute, Training Team United Kingdom);|
|Short Abstract: EMBL-European Bioinformatics Institute develops and maintains a variety of data tools and resources for application across the life sciences. Our training programme provides a mechanism for people to learn about these resources and gain hands-on experience from tool developers. Increasingly however, we are also being called upon to provide thematic and subject-specific material, giving trainees an opportunity to discuss the challenges of applying these tools in the context of their own research.
As the demand for training escalates and the diversity in background knowledge of our trainees widens (many of whom are bench scientists), the design of courses to meet this need becomes ever more challenging. A move away from traditional training techniques towards innovative approaches is required to address these challenges.
In response, we are exploring two new approaches to our training delivery:
1. Blended learning – by combining our face to face training with our “Train Online” course materials, we can provide a background level of knowledge for trainees pre-course and offer further support through advanced online provision post–course.
2. Building pipelines / workflows and use-case scenarios into our courses to enable trainees to contextualise their learning, facilitating the development of a reflexive learning environment thereby allowing trainees to explore the issues surrounding particular approaches in-line with their subject interests.
Incorporation of these methods into our existing course programme will further enhance the learning experience of our course participants, and allows us to provide the flexible approach necessary to meet the diverse needs of our trainees.
|Poster - D10|
|Challenges involved in developing a dynamic e-learning platform for EMBL- European Bioinformatics Institute
|Sarah Morgan, EMBL-European Bioinformatics Institute, United Kingdom
|Mindi Sehra (EMBL-European Bioinformatics Institute) Mindi Sehra (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom); Katrina Pavelin (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom); Joseph Rossetto (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom); Thomas Laurent (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom); Sarah Morgan (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom); Cath Brooksbank (EMBL-European Bioinformatics Institute, Web development/Web production United Kingdom);|
|Short Abstract: E-learning plays an increasingly important role in the continuing professional development of life scientists. The availability of high quality web-based courses provides researchers with an effective means of gaining new skills and knowledge whenever they have a few moments to spare.
Train Online (www.ebi.ac.uk/training/online) is a free web-based learning resource produced by EMBL- European Bioinformatics Institute. It contains a range of courses, from quick tours and in-depth walk-through guides on EMBL- EBI databases to video-based courses on analysis of sequence data.
As data resources and research applications change, so too must the associated learning resources. Keeping these up to date is a constant challenge that relies upon maintaining a close working relationship between the e-learning team and the scientific experts, creating timely and cutting-edge courses catering for a range of learning styles.
Widespread user engagement is key, so Train online makes no prior assumption about its users’ knowledge about EMBL- EBI resources. Instead, users are guided through subject-focused material at a range of skill levels. A combination of tutorials, guided examples, exercises and quizzes allows users to learn at their own pace, at any time, across the globe.
We encourage those who have attended face-to-face sessions to use Train Online to reinforce their learning once formal training has ended. Use of Train online does not require registration, but many users choose to register with us so that they can be updated as we continue to develop new online courses.
|Poster - D11|
|Bioinformatics training & education: towards global sustainable solutions
|Vicky Schneider-Gricar, The Genome Analysis Centre, United Kingdom|
|Nicola Mulder (Computational Biology Group, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Clinical Laboratory Sciences South Africa); David Lovell (CSIRO, Mathematics, Informatics and Statistics Australia); Celia van Gelder (NBIC- Netherlands Bioinformatics Centre , CMBI - Centre for Molecular and Biomolecular Informatics Netherlands); Fran Lewitter (Whitehead Institute for Biomedical Research, Bioinformatics and Research Computing United States); Manuela Helmer Citterich (University of Rome_TORVERGATA, Centre for Molecular Bioinformatics Italy); Pedro Fernandes (Instituto Gulbenkian de Ciência, Training Portugal); Judit Kumuthini (Centre for Proteomic and Genomic Research, Bioinformatics South Africa); Lonnie R. Welch (Ohio University, Bioinformatics Laboratory United States); Marie-Claude Blatter (SIB Swiss Institute of Bioinformatics, Swiss-Prot communication team Switzerland); Marc Robinson-Rechavi (University of Lausanne, Department of Ecology and Evolution Switzerland); Tommi Nyrönen (CSC - IT Center for Science, Development Finland); Erik Bongcam-Rudloff (Swedish University of Agricultural Sciences, SLU-Global Bioinformatics Centre Sweden); Bruno A. Gaeta (The University of New South Wales, School of Computer Science and Engineering Australia); Pascale GAUDET (SIB Swiss Institute of Bioinformatics, neXtProt Switzerland); Catherine Brooksbank (EMBL-EBI, Training United Kingdom); Rafael C. Jimenez (EMBL-EBI, Proteomics Service Team United Kingdom); Patricia M. Palagi (SIB Swiss Institute of Bioinformatics, Proteome Informatics and Evolutionary Bioinformatics Groups Switzerland); Michelle D. Brazas (Ontario Institute for Cancer Research, Knowledge and Research Exchange Canada); Aidan Budd (EMBL-Heidelberg, Structural and Computational Biology Germany); Javier De Las Rivas (Cancer Research Center (IBMCC, CSIC/USAL), Bioinformatics and Functional Genomics Group Spain); Manuel Corpas (The Genome Analysis Centre, Animal and Plant Genomes United Kingdom); Francis Ouellette (Ontario Institute for Cancer Research, Toronto, Ontario, Canada, Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada Canada); Via Allegra (University of Rome-La Sapienza, Biocomputing Italy); Teresa K. attwood (The University of Manchester, Faculty of Life Sciences & School of Computer Science United Kingdom);|
|Short Abstract: Bioinformatics education and training is in strong demand. Undergraduate and postgraduate students are discovering that they lack the necessary training to use bioinformatics tools and databases – to which their daily work increasingly exposes them – most effectively. While ‘high-throughput biology’ is transforming the bioinformatics research landscape, many bioinformatics degree programmes are closing down, leaving the resulting educational gaps to be filled with a variety of short, ad hoc, geographically dispersed training courses. The emergence of this ‘new biology’ is challenging trainers and educators not only to cover basic bioinformatics concepts during their courses, but also to stay abreast with new technologies as they emerge (e.g. NGS). Here, the problems are particularly acute, given the speed of turnover of the under-pinning technical platforms, coupled with the dearth of easy-to-use Web interfaces to the relevant analysis tools – users with no command-line experience are left struggling to keep up.
To tackle some of these issues several trainers, organisations, networks, societies and individuals around the world have joined forces to create a unique new Global Organisation for Bioinformatics Learning, Education & Training, GOBLET (www.mygoblet.org). The goal of GOBLET is to coordinate and consolidate world-wide bioinformatics training activities: to share, not duplicate, effort; to share, not duplicate, cost; to work together in a mutually respectful way towards common solutions and a sustainable future.
Here we outline the wider mission of GOBLET, its partners, its relationship with European training efforts through ELIXIR, and its achievements to date; including a brief review of its online training portal.
|Poster - D12|
|HUB: Heidelberg Unseminars in Bioinformatics
|Agnes Hotz-Wagenblatt, Deutsches Krebsforschungszentrum, Germany|
|Adam Gristwood (European Molecular Biology Laboratory, SCB Germany); Janos Binder (European Molecular Biology Laboratory, SCB Germany); Kristoffer Forslund (European Molecular Biology Laboratory, SCB Germany); Gideon Zipprich (Deutsches Krebsforschungszentrum, TBI Germany); Grainne Kerr (Deutsches Krebsforschungszentrum, Signaling and Functional Genomics Germany); Jonathan Fuller (Heidelberg Institute for Theoretical Studies, Molecular and Cellular Modeling Germany); Matthew Betts (University of Heidelberg, Protein Evolution Germany); Damien Devos (University of Heidelberg, Center for Organismal Studies Germany); Micheal Eichenlaub (University of Heidelberg, Center for Organismal Studies Germany); Aidan Budd (European Molecular Biology Laboratory, SCB Germany);|
|Short Abstract: HUB (Heidelberg Unseminars in Bioinformatics) is a forum for supporting and enhancing the community of people interested in bioinformatics and computational biology in the Heidelberg area. It focuses on two-hour bi-monthly meetings aiming to enhance relationships and enable people interested in bioinformatics to get to know each other better. Additionally (i) coordination meetings held are used to collect and discuss results and feedback from previous meetings, and to plan future HUBs (ii) the project's wiki http://hub-hub.de is used to coordinate ideas and feedback and plans for future meetings.
HUB meetings are collaborative and community-driven, and provide opportunities for scientists, and local institutions, to present their work in short talks. However, the main focus is on group-based activities, typically involving building collaborative projects that could produce tangible outcomes benefiting the participants e.g. one meeting in 2012 focused on collecting opinions on the key challenges for bioinformatics via a world-cafe style event, resulting in a publication in EMBO Reports doi:10.1038/embor.2013.34.
HUB members tell us that they are involved in the project because it:
- provides a positive, supporting environment to welcome newcomers to the community
- gives an opportunity to learn new ideas and perspectives on bioinformatics issues in an informal setting
- expands our social and professional networks in a fun way
- provides a forum to learn about professionally-relevant local institutions
- helps developing collaborations
- is a good context to learn about ways of organizing engaging, successful meetings
- gives valuable contacts and ideas for career development
|Poster - D13|
|A Training programme focuses on “Big Data”: From infrastructure needs to concepts and skills to handle, retrieve and analyse the data.
|Vicky Schneider-Gricar, The Genome Analysis Centre, United Kingdom|
|Allegra Via (University of Rome, La Sapienza, Biocomputing Italy); Rob Davey (The Genome Analysis Centre, Core Bioinformatics United Kingdom); Bernardo Clavijo (The Genome Analysis Centre, Computational Genomics United Kingdom);|
|Short Abstract: As many other Institutions and Universities across the globe The Genome Analysis Centre (TGAC) has daily requests for training at post-graduate level on BIG DATA, particularly on how to design, implement and analyse Next Generation Sequencing (NGS) data. In order to share the in-house expertise as well as collaborators expertise (in genomics-from sequencing to assemblies and data analysis- and bioinformatics-from infrastructure, computing to resources and tools) a series of activities have been designed to tackle many of the challenges involved in NGS training. The Training programme spans from best practice in programming for those with a biological background that have become (often self-learners) the “bioinformatician” in their groups as well as those with no command line proficiency that have started to work on this field. In this poster we present the structure and learning paths we have constructed based on “training needs” analysis across a variety of audiences. We also share ideas and successful stories on how to ensure Bioinformatics Training is sustainable and long term beneficial to all, those learning as well as the actual trainers.|
|Poster - D14|
|Molecular movies and the collective imagination
|Monica Zoppè, Scientific Visualization Unit - LTGM, Italy|
|Short Abstract: Scientific education has always made large use of imagery and symbols to explain concepts and to represent invisible objects.
The abundance of structural information on cellular components, and the availability of computer graphics instruments of high capabilities, makes it possible to build movies representing 'stories' beyond the limit of visibility, from cells to organelles to single molecules and metabolic events.
The choices made today in the representation of molecules, particularly those used in education in the schools and in other 'infotainment' situations (movies for the young, documentaries, advertising material referring to molecular reactions) are shaping the collective imagination of the scientists and the general public of tomorrow.
We consider it possible to convey scientifically relevant information in an intuitive way, using instruments developed for the entertainment industry, adapted to work with structural information (files in the pdb format, molecular dynamics trajectories, normal mode analysis data).
We will show some of our recent movies, that have raised the interest in the educational, artistic, technical and scientific communities, and describe the philosophy and the instruments behind them.
We suggest that this kind of representation can have a major role in the understanding by schoolchildren and by the general public, of complex biological issues, and in the support for science. However, we consider it important that a set of common guidelines is applied by all those that engage in the production of such movies.
|Poster - D15|
|Best practices in programming
|Patricia M. Palagi, SIB Swiss Institute of Bioinformatics, Switzerland|
|Franz-Josef Elmer (SIB Swiss Institute of Bioinformatics, ETHZ, D-BSSE Switzerland); Frédérique Lisacek (SIB Swiss Institute of Bioinformatics, Proteome Informatics Group Switzerland); Chandrasekhar Ramakrishnan (SIB Swiss Institute of Bioinformatics, , ETHZ, D-BSSE Switzerland); Marc Robinson-Rechavi (SIB Swiss Institute of Bioinformatics, , UniL Switzerland); Hannes Schabauer (SIB Swiss Institute of Bioinformatics, , UniL Switzerland); Milan Simonovic (SIB Swiss Institute of Bioinformatics, , University of Zurich Switzerland); Jakub Straszewski (SIB Swiss Institute of Bioinformatics, , ETHZ, D-BSSE Switzerland); Bernd Rinn (SIB Swiss Institute of Bioinformatics, , ETHZ, D-BSSE Switzerland);|
|Short Abstract: The SIB workshop “Best practices in programming” (BPP) emerged from an collaborative exercise leading more than 50 bioinformaticians to collectively define notions of “good” and “minimal” programming skills in bioinformatics. The target audience of BPP is bioinformatics or life sciences students and scientists who write software as part of their contribution to bioinformatics, but have no formal training in software engineering. The tutors are SIB members willing to share their expertise. The objectives are to help the aspiring and practising programmers to avoid the most common mistakes when writing scientific software, to improve the quality of their code, and to introduce skills and techniques for effective software development and sharing. Two BPP workshops have already taken place in the past 2 years. They covered aspects such as "Version Control", "Unit Testing", "Readable and Maintainable Source Code", "Code Refactoring". The major challenges of the BPP workshops are: how to structure the course for a diverse and heterogeneous audience, how to deal with the programming language barrier, and how to meet a wide range of needs when the overall goal is to guide the participants' everyday work with only little transfer. In this poster, we will present the experience from these two implementations and open the discussion of “how good is good enough” for a larger audience.|
|Poster - D16|
|Open platform for personalized mass education (POEME) and 4P education
|julie thompson, University of Strasbourg, France
|Julie Thompson (University of Strasbourg) Pierre Collet (University of Strasbourg, Icube France);|
|Short Abstract: In 2012, millions of students enrolled in the MOOCs (Massive Open Online Courses) proposed by renowned universities (mooc-list.com). Using only a computer and internet, students can attend seminars, do exercises and address difficult problems together with other distance learners. MOOCs are also impacting bioinformatics training, for example at bioinformatics.ca. The MOOCs represent a first step towards 4P (Participatory, Predictive, Preventive and Personalized) education:
• Students participate in their assessment, evolve optimized paths through the course modules and modify the content,
• Student profiles can be identified, which can then be used to predict the best educational path for new students,
• Educational content can be proposed to prevent the appearance of shortcomings in particular students,
• The result is a personalized path through the MOOCs.
We present the participative MOOCs that we are using to establish an educational ecosystem for the French Numerical Campus for Complex Systems. The ecosystem represents a model for the new online resources we are developing to complement our traditional continuing education courses, in order to teach bioinformatics, genomics and proteomics to life science and biomedical researchers.
Our open platform for personalized mass education (POEME) incorporates an Ant Colony Optimisation (ACO) technique to help students visit various e-learning items. ELO rating (used in chess competitions) is used to rate the e-learning items, refine the model and propose suitable items. ELO also represents a powerful audit system to track semantic problems in exercises. The dynamic and emerging content in POEME is designed to promote better access, exploitation and ultimately, generation of knowledge.
|Poster - D17|
|Ukufunda Integrated e-Learning and Training Resource for Proteomics, Genomics and Bioinformatics Support
|Judith Kumuthini, Centre for Proteomics and Genomic Research, South Africa
|Benjamin Kumwenda (Centre for Proteomics and Genomic Research) Judit Kumuthini (Centre for Proteomics and Genomic Research, Bioinformatics South Africa); delita Otto (Centre for Proteomics and Genomic Research, Bioinformatics South Africa);|
|Short Abstract: The ever-growing need for the use bioinformatics approaches to support industrial and academic research motivated the development of the Ukufunda integrated e-learning resource. There is a limited number of expertise to solve queries in these fields which is aggravated by the repetitive nature of queries; hence the need for technological innovation to extend support coverage and efficiency in responsiveness. Ukufunda which translates to ‘to learn’ in local language was developed to resuscitate several open-source e-learning platforms within the ‘omics’ fields that have been abandoned due to lack of funding following the economic melt-down. User behavior has significantly been changing over the years. It requires integration of e-learning resources with the social media to reach out to the current and future generations of Biologists and Bioinformaticians. Users usually struggle and spend so much time to find useful, credible and applicable information on the Internet as they jump from one website to another.
Ukufunda is a one-stop-shop of resources for genomics, proteomics, bioinformatics and statistics which also links to other additional biological databases and sites. It is a database driven web based resource which was developed using WordPress content management software that can be accessed by users over the Internet. It presents information in form of text, video clips and webnars in its current beta version. It is a repository for training and lecture materials that can be conveniently managed, accessed and shared by students and trainers.
|Poster - D18|
|Problem-Based Interdisciplinary Learning in an Undergraduate Computational Biochemistry Course
|Yosi Shibberu, Rose-Hulman Institute of Technology, United States|
|Mark Brandt (Rose-Hulman Institute of Technology, Chemistry & Biochemistry Department United States);|
|Short Abstract: We are creating a new interdisciplinary, undergraduate, computational biochemistry course. This team-taught course is organized around three main problems: i) protein sequence alignment ii) protein structure alignment and iii) normal mode analysis of protein structures using insulin as a model protein.
The six chemistry/biochemistry and four mathematics students currently taking the course found that creating a DNA sequence translation program was a challenging task, primary because each student wanted to complete the assignment independently. Subsequently, they have been working successfully together to creating a protein sequence alignment program that uses scoring matrices they derived themselves.
Developing a grading scheme that takes the different student backgrounds into account has proved to be challenging.
The most important improvement that we wish to make to this course is to use an inverted-classroom approach. We intend to create self-paced, on-line video and multimedia resources for course content outside of class in order to free class time for instructors to facilitate a higher quality interdisciplinary learning experience. Although the first attempt clearly has needed improvement, we think that this course will ultimately become a highly useful enhancement to the education of both mathematics and biochemistry majors.
|Poster - D19|
|Bioinformatics Knowledge Transfer Programme (KTP) for Human and Capital Development
|Benjamin Kumwenda, Centre for Proteomics and Genomic Research, South Africa|
|Judit Kumuthini (Centre for Proteomics and Genomic Research, Bioinformatics South Africa); Domenica D'Elia (EMBNet, Bioinformatics Italy); Ida van Jaarsveld (Centre for Proteomics and Genomic Research- Bioinformatics, Bioinformatics South Africa); Benjamin Kumwenda (Centre for Proteomics and Genomic Research, Bioinformatics South Africa);|
|Short Abstract: The multidisciplinary nature of the bioinformatics field, coupled with rare and depleted expertise, is a critical problem in the advancement of bioinformatics in Africa. Further impediments include limited internet connectivity, lack of computational resources and sub-standard research facilities. Individuals who receive international training in highly resourced environments usually struggle to function or implement their expertise and knowledge when they return to their resource-stricken native environments. Short-term training programs have proved to be unsustainable and costly since knowledge and skills are not retained over time and limit the impact of such training.
The KTP is a research and education model conceptualised to address these problems in a sustainable manner to stimulate, enhance and strengthen African bioinformatics capacity. Its aim is to cost effectively facilitate the transfer of knowledge and skills from experienced, internationally recognised experts to local scientists. The CPGR, with its partners as hosts, facilitate the process by identifying experts, training requirements and potential research associates. Instead of several associates travelling to well established labs for short periods of time, experts are brought in to interact and conduct high-quality research agendas locally. Experts and associates are brought together to work on relevant projects through which transfer of knowledge and skills is achieved naturally. The advantage of the approach is that several associates benefit from one expert, while minimising travel and accommodation expenditure. The programme is assessed by project outputs such as number and quality of publications, conference participation, patents or intellectual properties secured and the number of successfully trained associates.
|Poster - D20|
|How to train biologists to analyze next generation sequencing data in two days
|Eija Korpelainen, CSC - IT Center for Science, Finland|
|Aleksi Kallio (CSC - IT center for Science, Application Services Finland); Taavi Hupponen (CSC - IT center for Science, Application Services Finland); Petri Klemelä (CSC - IT center for Science, Application Services Finland); Kimmo Mattila (CSC - IT center for Science, Application Services Finland); Ari-Matti Saren (CSC - IT center for Science, Application Services Finland); Matti Kankainen (CSC - IT center for Science, Application Services Finland); Mikael Karlsson (CSC - IT center for Science, Application Services Finland); Massimiliano Gentile (Blueprint Genomics, Bioinformatics Finland); Jarno Tuimala (RS Training, training Finland); Ilari Scheinin (VU University Medical Center, Department of Pathology Netherlands);|
|Short Abstract: Training biologists to analyze next generation sequencing (NGS) data can be challenging, because they typically don’t have command line or programming experience and cannot spend much time away from the lab. In order to enable efficient training and subsequent use of NGS and microarray data analysis tools, we have developed the biologist-friendly open source software Chipster (http://chipster.csc.fi/).
Chipster offers an intuitive graphical user interface to over 250 commonly used analysis tools. It takes care of file format conversions and contains a built-in genome browser, making it easy to move from task to another. Users can share analysis sessions, allowing trainers to prepare example sessions which are easy to grasp thanks to their visual overviews.
We have run over 50 courses with Chipster on three continents, and the feedback has been positive. Serving analysis tools in a unified and user-friendly manner enables us to concentrate on teaching the actual data analysis methods. The courses consist of intertwined lectures and hands-on exercises, allowing students to try their new skills in practice straight away.
When students start analyzing data independently after the course, they can contact the trainer easily using Chipster’s Contact support –functionality, which automatically adds the current session with all data and log files to the contact request. Trainers can also monitor usage patterns with Chipster’s admin console, which can quickly identify tools that seem problematic to users.
Taken together, Chipster is a free and biologist-friendly software which enables efficient training of life scientists in NGS and microarray data analysis.
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