Systems training in maths informatics and computational biology (SySMIC)
Lead Research Organisation:
The Open University
Department Name: Faculty of Sci, Tech, Eng & Maths (STEM)
Abstract
Amongst others Sir Martin Rees, the President of the Royal Society, has stated that 'the problems of physics are the problems of scale, the problems of biology are the problems of complexity.' This keen insight captures a profound truth about the traditional divide between scientific disciplines. Traditionally mathematics and computing have been powerful allies in the elucidation of the problems of physics but while effective in biology they are not so widely used. For most of modern history the complexity in living systems has not been routinely unapproachable with mathematics and computing - either too little biology was well enough described, the appropriate maths tools did not exist or the performance of computers was too slow. This has all changed recently and now it is time to take maximum advantage. While the BBSRC and other agencies in the UK and institutions around the world have made great investments in specialist research centres it is now time to mobilise the larger mass of UK bioscientists. Biologists of all disciplines, working from the scale of atoms and molecules to that of living ecosystems, must make their contribution and provide their hard-won biological insight to complement the efforts of mathematicians, computer scientists, physicists and engineers who are already exploring the new territory in the emerging discipline of systems biology. To be effective biologists must learn to speak the common language of the physical and engineering science - applied mathematics and computing. They must learn to apply their skills without hesitation and to engage with the other scientific disciplines enthusiastically - SysMIC will start to make this possible. The SysMIC project's over riding aim is to enable rapid and effective 'up-skilling' of a large body of biologists and to accelerate their entry into systems biology and drive the successful study and manipulation of complex biological systems.
Technical Summary
We will create a programme consisting of three distinct modules and deliver them via a bespoke Virtual Learning Environment (VLE), customised for the BBSRC, using Moodle. The aim is to allow 'students' from all levels of research activity - from new graduate students to senior PIs and lab or institute heads - to grasp the power of mathematical and computationally-driven model building to clarify biological problems of great complexity. We wish systems modelling to become routine in UK bioscience research with investigators at all levels readily creating and refining 'first-pass' or 'toy' models whenever they are faced with biological problems composed of the interaction of distinct parts. There is no other way to uncover the rules governing the emergent properties that define living systems from the molecular to the ecological scale. We will combine unique resources and expertise embedded in the member institutions of the SysMIC consortium - unsurpassed expertise in the teaching of mathamatics at a distance from the Open University; high-powered systems biology research and teaching from the BBSRC/EPSRC Systems Biology Centre in Edinburgh; mathematical and systems biological insight embedded at the first-rate bioscience and biomedical research environment at UCL and the backbone of expertise at Birkbeck College London in the delivery of high-level, technically oriented, biology through the web. Through training to use Mathematica routinely in order to lighten the burden of attacking complex problems our 'graduates' will be accelerated into systems biology study and its application to research. During the course students will move from mathematical basics to encounter their application to complex systems biological analysis through open-ended modelling projects based on real-world problems and previously validated studies.
Planned Impact
Systems biology approaches allow the analysis of complete system behaviour, identifying robust and sensitive components and so targeting experimental power to areas with greatest potential impact and limiting wasted analysis. Some of society's current research challenges, from sustainable bioenergy to food security will only be solved by integrated research and so supporting bioscientists in developing these capabilities has the potential to yield very significant research impact. Interestingly, experience also demonstrates that the wider application of modelling techniques will yield new computational and mathematical challenges, thus driving forwards research in informatics and computer science. A major output from this e-learning initiative will be a trained cadre of mathematically- and computationally-literate biologists. The training provided by the SysMIC programme has the potential to reach a significant number of bioscience researchers at all levels of the career pathway. Our use of cutting edge case studies, developing in complexity through the staged learning materials, will give 'graduates' exposure to the real world application of modelling. We aim to equip researchers to develop their own preliminary models for any and all systems of interest. In the longer term this training will deliver impact identified by an increasing number of multiple Principal Investigator, potentially multiple institution, but definitely cross-disciplinary funding applications submitted to the BBSRC in responsive mode. Furthermore, developing researchers to adopt and understand systems approaches in their research will increase the opportunities for junior researchers interested in systems biology. Equipping these researchers with the ability to interact, collaborate and operate successfully across traditional discipline boundaries will drive a culture change in the employment trajectories of postdoctoral researchers. As the funding environment continues to evolve we expect that researchers who have undertaken the SysMIC programme will be better able to compete and deliver complex interdisciplinary research programmes, skills which will directly enhance their career progression. This consortium has also developed plans for private sector training, compatible with primary BBSRC responsibilities. Through relationships with Knowledge Transfer Networks, existing systems-based industry collaborations and leveraging the vast expertise of institutional Technology Transfer Offices we will promote controlled industry access to the training programme. Overall, this consortium represents a strategically significant grouping of institutional expertise, an exciting link between a Centre for Integrative Systems Biology and the wider UK research and teaching community and is an unparalleled opportunity to deliver a cost-effective e-learning initiative with far-reaching and transformative impact.
Organisations
Publications
Description | The grant supports the development and delivery of a comprehensive online course in mathematics and computational methods used in systems biology. It has been developed by a consortium of researchers at UCL, Birkbeck, Edinburgh and the Open University. The course consists of three modules: Module 1: Basic Skills, Module 2: Advanced Topics and Applications, and Module 3: Project Work. The software used in this course is MatLab. The first cohort of students started on the Module 1 in January 2013, while the second and third modules were being further developed. Module 2 has now also seen several cohorts of students. The modules have been revised following feedback from students. As of October 2013, over 500 students had entered the course, rising to over 800 by mid 2014, and we have now surpassed the original target of 1250 students with 1445 students enrolled on module 1 by October 2016. There have also been a few successful projects on module 3. New Moodle tools have been developed to monitor cohort and individual progress. We recently started to convert MatLab code into Python to be able to offer the course with different software. Further plans under development concern finalising preparing an additional entry module and publishing modules in book form. The modules have proved very successful and attracted additional, fee-paying customers. The UCL team won the UCL Provost Teaching award under the Team Collaboration and Achievement category in June 2015. A paper describing the SysMIC approach has been prepared and published as a PeerJ Preprint, and is available at DOI: 10.7287/peerj.preprints.2523v1. Despite the end of funding, the modules continue to be taught. Unfortunately there is no appropriate category in the list of outputs provided by researchfish, so it is a bit difficult to provide comprehensive information using this system. Update: Several years after the end of the funded period, SysMIC continues strongly. Our biggest ever cohort got underway in May 2020. We are also considering to expand further into data science, and are currently testing a new 1-month component in elementary data science: Data Handling, Supervised ML (Classification ) and Unsupervised ML (Clustering). |
Exploitation Route | It is conceivable that the material could be adopted by industry for training employees. This possibility is being investigated by the SysMIC consortium. The course was mainly directed at BBSRC-funded research students in the first instance, but has already reached a wider audience, and we are actively seeking to increase our reach. This includes academic institutions in the UK and abroad, as well as the non-academic sector. We are currently set to keep the course running and to develop it further after the end of the initial funding period. Depending on how successful the recruitment of students on the module is, it may become a long-term resource supporting the analytical skills of researchers in life science and related disciplines. |
Sectors | Agriculture Food and Drink Education Pharmaceuticals and Medical Biotechnology Other |
URL | http://SysMIC.ac.uk/ |
Description | The project educates new generations of researchers in systems biology in the use of mathematics and statistics. The expected impact is through future research of these researchers, building on the expertise acquired by working through the module(s). A summary of the achievements has been published by the consortium as a PeerJ preprint 2523 in 2016: "SysMIC: A Blueprint for interdisciplinary online training in the life sciences", Authors: Gerold Baier, Chris Barnes, David Crowe, Stephen Gilmore, Uwe Grimm, Philip Lewis, David Morse, Clare Sansom, Robert D. C. Saunders, Adrian Shepherd, Geraint Thomas, DOI:10.7287/peerj.preprints.2523v1 |
First Year Of Impact | 2016 |
Sector | Education |
Title | SysMIC Module 1 first on-line cohort complete. SysMIC module 2 materials completed |
Description | Approximately 150 students entered SysMIC Module 1 between October 2012 and January 2013 and studied until June 2013. Approximately 55% of entrants had completed the module and received their completion certificate by August 2013. SysMIC module 1: basic skills has been taught to the first on-line cohort (after previous trial run at UCL) of students, with generally positive feedback. A number of cohorts have since taken the module. SysMIC module 2: Advanced Topics and Applications was completed and published, several cohorts have now taken this module. There have also been a few participants on the project module 3. |
Type Of Technology | Software |
Year Produced | 2012 |
Impact | SysMIC training has contributed to some publications, in particular for participants on module 3. |
URL | http://sysmic.ac.uk/ |
Title | SysMIC Modules produced and delivered |
Description | Module material was developed and taught to cohorts of PhD students in Systems Biology, teaching students mathematics, statistics and modeling skills. A total of 1445 students had enrolled on module 1 by October 2016, of which 683 had successfully completed the entire module. Module 2 had 252 enrolled participants, of which 109 had completed at the time. As for reasons of non-completion, 77% of a survey of 101 participants cited time reasons as the main issue. The modules were supported by a number of workshops and day schools which were well attended and received excellent feedback. There have also been some students on the individual support module 3, with some publications arising as a result. With the end of BBSRC funding approaching, the SysMIC team approached DTPs and secured a number of commitments for places for future presentations of the material, which will make it possible to continue to offer this resource at least for the short-term future. There has also been success in attracting other participants, for instance from the Francis Crick Institute, and we hope to continue to attract a wider audience as word spreads. The consortium will continue to work together after the end of the current funding, and is actively seeking follow-up funding from a variety of funders. The development of further resources, such as lower level entry type material, is also in progress. |
Type Of Technology | Software |
Year Produced | 2016 |
Impact | Cohorts of students who have engaged with the material have a much improved knowledge of analytic tools for modeling and describing biological systems. |
URL | http://sysmic.ac.uk/ |