Needs for Training in Neuroinformatics

1st INCF Workshop on Needs for Trainingin NeuroinformaticsJuly 23-25, 2008 - Edinburgh, United Kingdom

1st INCF Workshop on Needs for Training in NeuroinformaticsJuly 23-25, 2008School of Informatics, University of EdinburghScotland, United KingdomAuthorDavid WillshawScientific OrganiserDavid Willshaw, University of Edinburgh, Edinburgh, United KingdomWorkshop ParticipantsAd Aertsen Bernstein Center for Computational Neuroscience (BCCN), Freiburg, GermanyDagmar Bergmann-Erb BCCN, Munich, GermanySimone Cardoso de Oliveira BCCN coordination, Freiburg, GermanyPeter Dayan Gatsby Computational Neuroscience Unit, UCL, UKKenji Doya Okinawa, JapanPiotr Durka Warsaw, PolandGary Egan Melbourne, AustraliaGaute Einevoll Aas, NorwayJeff Grethe Biomedical Informatics Research Network (BIRN), UCSD, USARolf Kötter Radboud University, Nijmegen,NetherlandsKit Longden Imperial College London, UKRisto Näätanen Århus, Denmark & Helsinki, FinlandBarry Richmond NIH, Bethesda, USARaphael Ritz INCF Secretariat, Stockholm, SwedenArjen van Ooyen Amsterdam, NetherlandsMark van Rossum Edinburgh, UKJonathan Victor Weill Cornell, USAHui Wang INCF Secretariat, Stockholm, SwedenDavid Willshaw Edinburgh, UKKevan Martin (Zurich, Switzerland) was unable to attend the workshop but has been involved in drafting the report.Scribes at discussion sessions: Catherine Ojo, Ian Saunders, Nicolas Heess, Edinburgh, UKThe following also contributed to the report:Hirsch Cohen Sloan-Swartz Foundation, USAErik De Schutter Okinawa, JapanJim Bednar Edinburgh, UKSupported by the European Union Special Support Action INCF, the Swedish Foundation for Strategic Research andthe INCF Central Fund2

Contents1 Executive Summary 42 Introduction 52.1 Workshop 52.2 The scope of neuroinformatics & training 62.3 Target groups 63 Current Provision 74 Needs for Neuroinformatics Training 74.1 Training for a PhD 74.2 Short courses 95 Recommendations 105.1 Outreach and publicity actions 105.2 Web-based training portal 105.3 Support of short courses 105.4 Training visits 115.5 Novel funding schemes 115.6 Future workshops about training 115.7 Coordination of training issues at INCF level 11Appendix A: Current Teaching Provision 12A1 Group 1 (undergraduates) 12A2 Group 2 (Masters students) 12A3 Group 3 (PhD students) 14A4 Group 4 (postdoctoral researchers) 16A5 Group 5 (Academic staff ) 17Appendix B: Links to Relevant Web Sites 18Appendix C: Workshop Programme 19 3

1 Executive Summary At this workshop the needs for training in neuroinformatics in the context of the current opportunities and challenges were discussed. The delivery of two types of training was of particular interest. (i), Given that neuroinformatics requires the acquisition of knowledge from different disciplines, generally it is best for students to acquire the necessary background at the Masters level. Neuroinformatics Masters courses are an appropriate training medium for PhD students before embarking on their research; an ideal PhD course in neuroinformatics is described. (ii), PhD students who cannot profit from substantial Masters level training, researchers entering at the postdoctoral level and, in prin- ciple, academic staff, will all benefit from suitable short courses, which can range from a fraction of a day to a few weeks in duration. Seven recommendations for the INCF were made, aimed at improving the provision of the appropriate training at national and international levels. These include: the inclu- sion in the INCF Portal information about current training material and information about training material of all kinds: the development of new short training courses and the support of existing ones, the development of a specific programme in neuroinformatics training, as well as future workshops on training. A list of the current training provision known to participants is contained in Ap- pendix A and Appendix B gives a set of Web links relevant to neuroinformatics training issues.4

2 IntroductionNeuroinformatics, the new research field situated at theintersection of neuroscience and the physical sciences, isby its nature interdisciplinary.Neuroinformatics requires the integration of knowledgefrom mathematics, physics, computer science and engi-neering together with detailed knowledge of the nervoussystem. It is essential that neuroinformaticians should beable to communicate with researchers across the spec-trum of all relevant disciplines.Neuroinformatics poses a specific challenge for training,as this variety of knowledge and research cultures is onlyrarely combined in one single place and often falls at theboundaries of traditional academic departments.Given the broad scope of neuroinformatics, only fewcountries will be able to provide a wide range of neuroin-formatics training; this will require international coopera-tion. It is therefore essential to establish best practice inneuroinformatics training at the international level.2.1 WorkshopThese considerations make a discussion of neuroinfor-matics training a highly relevant subject for discussionby the INCF. In cooperation with the UK NeuroinformaticsNode, a 3-day INCF workshop was held in Edinburgh, UK,from 23rd to 25th July 2008. The intention was to discussthe best training for preparing neuroinformatics studentsfor successful work in the academic, clinical or industrial/technological context. The four key aims of the workshopwere to:1. Establish the different target groups requiring training.2. Establish a profile of the current provision for training.3. Discuss needs for training and how this training should best be delivered.4. Develop a set of recommendations for the INCF Board and thereby for national agencies and funding bodies.The workshop was structured around a number of dis-cussion sessions preceded by scene-setting talks by par-ticipants. This report is based on the summary reports ofthese discussion sessions. 5

The report is written for the Governing Board of the INCF. (h) Large scale, reusable software development andWe hope that it may also be useful to the neuroinformat- parallel implementationics scientific communities and national decision-making (i) Machine learning techniquesand funding bodies. 2.3 Target groups2.2 The scope of neuroinformatics & train-ing Five different target groups for neuroinformatics training were identified, each with different training needs:Neuroinformatics is concerned primarily with the appli-cation of methods from the physical sciences, such as Group 1: Undergraduatesmathematics, physics, computer science and engineer- Group 2: Graduate students following a Masters courseing, to studying the nervous system. Group 3: PhD students Group 4: Postdoctoral researchersThe participants defined the following set of core compe- Group 5: Academic stafftencies of which at least basic knowledge is expected ofneuroinformatics researchers: The concept of defining separate undergraduate, Mas- ters and PhD programmes is essential to the European(a) Knowledge of the physiology, anatomy and biochem- Bologna process, which aims to develop standards for istry of the nervous system training in European higher education by 2010, and cor-(b) Knowledge of the brain at the systems/cognitive/ responds approximately to the prevalent training struc- psychological level ture in the USA.(c) Experience in working in a “wet” neuroscience lab(d) Mathematics at an advanced level including linear algebra, dynamical systems analysis(e) Knowledge of stochastic modelling, time series analysis, exploratory data analysis and applied statistics(f ) Ability to programme in high level languages(g) Knowledge of imaging techniques and image analysis(h) Familiarity with widely used neuron and network models(i) Knowledge of basic modelling techniques together with relevant simulatorsThere is a large range of additional specialised topics in-cluding, for example:(a) Bioinformatics/systems biology(b) Development of the nervous system(c) Theoretical biology(d) Brain/machine interface(e) Hardware applications(f ) Clinical applications(g) Computational neuroanatomy6

3 Current Provision 4 Needs for NeuroinformaticsAll workshop participants contributed information about Trainingthe training programmes known to them. From the dis- To carry out research requires the integration of differ-cussions the following picture emerged, shaped by the ent kinds of knowledge. It is difficult to train students sofact that neuroinformatics depends on training in differ- that by the end of their first degree they are equipped toent disciplines, the combination of which is not encoun- do neuroinformatics research, having acquired sufficienttered in conventional courses. knowledge of neurobiology coupled with the requisiteAt the undergraduate and Masters levels, most neuroin- mathematical and computational skills. To attain thisformatics training is delivered as part of another degree solely through an undergraduate degree programmeprogramme. At the undergraduate level, there are no de- requires several structural and social barriers to be over-gree courses at present; at Masters level there are a few. come. As described in Section A.1 of Appendix A, undergraduate programmes are emerging, which may help toSome PhD programmes offer a period of training before make undergraduate teaching of neuroinformatics a firmstudents embark on their research, either in a neuroin- possibility.formatics programme or in one in a related subject. Oth-erwise, PhD students acquire their training by attending • The best opportunity for training students forthe short courses available, which are of many different neuroinformatics research is through Masters leveltypes and duration. training following a first degree in the biological or the physical sciences.Most postdoctoral researchers and academic staff who • Similarly, researchers who switch into neuroinfor-receive training in neuroinformatics do so by attending matics at the postdoctoral level are most likely toshort courses. Others receive informal “training on the have acquired training in either the life sciences orjob” or acquire their knowledge through reading text the physical sciences and therefore need training inbooks or by browsing the web. While many of the lon- areas of research that are completely new to them.ger (more than a week) short courses are configured forPhD students and postdoctoral researchers, there are In the discussion at the workshop it was decided to con-no short courses designed for academic staff. However, centrate on the needs for two types of training: the train-there are funding schemes available for academics who ing required to carry out a PhD (Group 3), which maywish to shift disciplines, corresponding to the more spe- also be relevant to Masters students (Group 2); and thecific neuroinformatics-oriented fellowships available at training delivered in short courses, which is relevant to allthe postdoctoral level. groups at postgraduate level and beyond.The full list of current neuroinformatics training opportu- 4.1 Training for a PhDnities known to the participants is given in Appendix A. The overwhelming consensus was that to carry out neuroinformatics research, an extensive period of training is required. 4.1.1 Components of the ideal PhD course The ideal PhD course has the following components: 1. This is made up of an extended period of training (typically 1 or 2 years) followed by 3 years of research. This will serve the needs of Group 3. Students obtain a Masters degree after the training period. The taught component could also be used as a stand alone Masters degree (Group 2). 7

2. Formal recognition of the course by the training life sciences students will need mathematics at an ad- institution is essential, as it increases the chances of vanced level and the ability to programme in at least one attracting funding and other benefits enjoyed by higher level programming language such as MATLAB or properly constituted courses. Python. Students from the physical sciences require a basic knowledge of biology and neurobiology.3. The training should be flexible and cater to different student backgrounds. In particular, there should be Core courses: basic training in mathematical and computational techniques for life sciences students and training in (a) The physiology, anatomy and biochemistry of the basic biology for physical sciences students. nervous system4. There should be a core set of taught courses to- (b) How neurons interact, specifically their role in devel- gether with a larger set of more advanced courses opment, sensory processing, learning & memory from which the students choose. and motor systems5. There should be lab rotations. This is a way of mak- (c) Neural processes at the cognitive/psychological level ing students aware of the research being carried out (d) Imaging techniques and image analysis in the local environment and of potential supervi- sors. (e) Time series analysis and signal processing6. During the training, the students should have (f ) Data acquisition, storage and analysis techniques hands-on experience in at least one experimental (g) Common neuronal and network models, such as lab. Hodgkin-Huxley, integrate-and-fire neurons and7. There should be a range of additional activities, mean field models and their best known applica- such as the students being given introductory texts tions, such as in associative memory and sensory to prepare them for the course, journal clubs, and processing seminars on success stories in neuroinformatics. (h) Basic modelling techniques together with relevant8. Students should be encouraged to spend time in simulators such as NEURON and GENESIS another lab, preferably in another country. (i) Experimental design and model evaluation9. Students’ PhD topics should be decided at the end Optional courses: of the period of training, once the students have acquired knowledge of the subject and what is There is a large range of additional, specialised topics feasible within the specific environment. from which specialised options can be chosen, including:10. The thesis committee should contain at least one experimentalist and one theoretical/computational (a) Bioinformatics person. (b) Systems biology4.1.2 Contents of the taught component (c) Theoretical biologyThe taught courses relate closely to the basic competen- (d) Developmental neurobiologycies that a neuroinformatics researcher should have, asdiscussed in Section 1.4. (e) Functional neuroimaging and high density EEG/MEGPreparatory courses, to be studied by students to fill in (f ) Computational neuroanatomygaps in their undergraduate education, are followed by (g) Software development for neurosciencecore courses and then a set of electives, the contents of (h) Neuroscience databaseswhich depends on the local environment. (i) Information theory and neural codingPreparatory courses: The precise training will have to betailored to each student’s background. In broad terms, (j) Machine learning techniques, including Bayesian ap- proaches8

(k) Brain/machine interface • Many courses are chronically oversubscribed. This could be seen as a positive feature which allows(l) Neuroprosthetics organisers to select the optimal mix among moti-(m) Hardware applications vated students. However, this also means that many students do not obtain the much-needed training,In addition, it is important to have courses available ontransferable/soft skills, such as time management, paper • Most of the courses are expensive, which is anotherwriting, giving presentations, preparing posters, etc. barrier to student attendance, especially in labs that are new to neuroinformatics and so do not have the4.1.3 Practical issues of implementation funding available.At any particular university or research institute that of- • There is an uneven coverage of topics. For example,fers neuroinformatics training, local structural constraints there are few experimental neuroscience courseswill shape the actual course that can be constructed. which are accessible to non-biologists because of competition for places with life scientists. There areIn some universities it may be difficult to organise a de- no courses teaching neuroinformatics tools for datagree course across different departments or faculties, or base applications.it may be easier to cater to students exclusively from thelife sciences or the physical sciences, rather than from • There is no course designed specifically for academicsboth. who wish to learn about neuroinformatics; neither for physical scientists to learn about neuroscienceLocal research directions will define the content of the nor for biologists to learn about the mathematicaloptional courses to be offered to students and so it is to basis of computational methods. Academics dobe expected that different courses will acquire their own attend very short courses; organisers of coursesflavour. stretching over weeks tend not to select academ-Given the specific national and local constraints, some of ics because of their effect on community buildingthe essential components of this ideal course will be miss- amongst the much younger participants.ing in any particular programme. Cooperation between • While some of the annual courses have a securedifferent institutes is therefore desirable; for example, by financial basis, many do not. For example, the Euro-allowing students from other institutes to attend courses pean advanced course on computational neurosci-or to host student visits. ence has trained around 500 students over 13 years, yet it has been a struggle to obtain reliable funding4.2 Short courses from year to year.The workshop participants felt that short courses play anextremely valuable role in the education of PhD studentsand postdoctoral researchers. For both target groupsthey provide essential training that otherwise would beunavailable to the student or researcher. Short coursesshould be continued and expanded in type and number.Academics especially would profit from shorter tutorialsfor interested non-experts; particularly to introduce ex-perimentalists to novel ways of using their data. In ourrecommendation R3, we propose that the INCF takes partin this process. In addition, Recommendation R2 is thatthe INCF facilitates other methods of delivering training,particularly using the Internet.We found a number of shortfalls in the courses currentlyavailable, which need to be addressed: 9

5 Recommendations This will help students make their choices and also make teachers aware of other courses.Workshop participants made seven recommendations.R1 is a general recommendation about neuroinformatics; Given the current shortage of training opportunities, oth-R2 is about using the INCF portal. R3, R4 are about sup- er ways of providing training material are also needed.porting training, R5 is about funding schemes, and R6, The portal could contain relevant materials of many dif-R7 are about future activities looking at neuroinformat- ferent types (including those mentioned under 4.1), suchics training issues. Any measures that are adopted should as:encourage the increased involvement of women, who • Recorded talks in different formats, particularlyare insufficiently represented in the field. those suitable for the general public or high school students5.1 Outreach and publicity actions • Interviews with eminent people in the fieldA prime factor for the success of the INCF in developingand facilitating neuroinformatics worldwide is that neu- • Information about relevant text booksroinformatics becomes known beyond the confines of • Other self-study materials, such as sets of bench-the neuroinformatics community. mark data suitable for testing competence in aThere are at least six important groups who need to be particular techniqueinformed as to what neuroinformatics is, why it is impor- • Materials that could be used for training that relatetant and, in the present context, why it is important to to the areas in which the INCF has established work-develop neuroinformatics training. These are: ing groups.• Students at the Masters and undergraduate levels The portal could also be used to record information about and pupils in high school the destinations of students after training, valuable for• The basic and clinical neuroscience communities both course evaluation and for applications for funding. who are not involved in neuroinformatics This could be a resource for people wishing to organise follow-up networking.• Other related scientific communities such as those working in systems biology, computer science, Inspiration for using the INCF portal for training purposes physics, etc. can be gained from the Society for Neuroscience web- based neuroscience teaching portal at http://www.ndgo.• Commercial sectors such as pharmacology and com- net/sfn/nerve/. puting where neuroinformatics may find application• The general public Recommendation R2: that a section of the INCF portal be used for making material relating to neuroinformatics• Politicians and decision makers of funding agencies teaching universally available.Recommendation R1: that a professional science writerbe employed to develop one section of the INCF portal 5.3 Support of short coursesto contain a layperson’s guide to neuroinformatics top- It is crucial that the current short courses be maintainedics, including academic success stories, interesting CVs of and expanded, in terms of the number of places avail-leading neuroinformatics figures, and sets of FAQs. able and the coverage of themes and target groups (such as academic staff, for which no course exists). The INCF5.2 Web-based training portal should undertake an initiative to ascertain where theThere is great scope for using the INCF portal to aid neu- need is most prominent and should facilitate and supportroinformatics training. courses, financially where possible. In addition, the INCF could develop or support existing or new annual coursesIt could provide details of all current undergraduate, Mas- in areas of need. It is strongly recommended that such aters, PhD courses, short courses and training seminars course be organised immediately before or after the an-available and as much of their contents as is possible. nual Neuroinformatics Congress.10

Recommendation R3: that the INCF identifies short would be the organisation of placements in industry.courses that are needed, coordinates funding initiatives,develops new courses, and supports existing courses fi- Recommendation R6: that future workshops on trainingnancially. issues be organised, particularly one to discuss training issues relating to clinical and industrial applications and5.4 Training visits in which clinical and industrial representatives take part.In the discussions at the workshop, the importance of 5.7 Coordination of training issues at INCFstudents having experience of different research envi- levelronments was emphasised. This would be one way fortheoreticians to experience experimental neuroscience. We recommend that the INCF establish an INCF activityWe recommend that the INCF encourages institutions to in the area of training. This would involve the formationinitiate schemes for training visits, advertises such op- of the respective committees and planning a set of activi-portunities (see R2) and makes funds available for such ties. There is a need for a person at the INCF Secretariat tovisits. be directly responsible for training matters.Recommendation R4: that the INCF develops a scheme of Recommendation R7: that an INCF Programme be set upvisits for training purposes and sets up a site on which re- and a designated person at INCF Secretariat be respon-quests and offers can be posted. sible for the coordination of matters concerning neuroinformatics training.5.5 Novel funding schemesThere are national funding schemes that support neu-roinformatics training which could well be adopted byother countries.Examples of suitable schemes are:• Many, but not all, national bodies provide explicit funding for PhD programmes• Some countries run fellowship schemes that enable researchers to enter neuroinformatics at the postdoctoral level• Discipline hopping schemes enable academic staff and postdoctoral researchers to change fieldsRecommendation R5: that the INCF collects and evalu-ates information about novel funding schemes that po-tentially are applicable to neuroinformatics; and that theINCF encourages funding agencies to adopt or maintainthose schemes that have been proven successful.5.6 Future workshops about trainingAs representatives of the academic basic science com-munity, workshop participants felt that there were othertopics that have an impact on neuroinformatics trainingthat could be discussed at a separate workshop. Of par-ticular interest was the possible application to clinicalneuroscience and to commerce and industry, particu-larly the pharmacological sector. One subject to discuss 11

Appendix A: Current Teaching Pro- undergraduate degree in Information Engineering with a minor in neuroscience and genetics.vision The Division of Biophysical Engineering, Department ofThe current teaching provision is described by giving ex- Systems Science, Osaka University, Japan offers an under-amples of what are known to the participants as highly graduate course combining biological and physical sci-respected programmes. It was not the intention, nor was ences teaching, including neurophysiology, cell biology,it possible, to give an exhaustive list. signal processing and computer programming.A1 Group 1 (undergraduates) A1.3 Neuroinformatics courses as a small part of aA1.1 Degree programmes in neuroinformatics degree programmeCurrently there is no undergraduate programme in neu- Despite this lack of formal courses, many students gainroinformatics. There is a BSc course under development a valuable introduction to neuroinformatics by studyingand due to be launched at Warsaw in Autumn 2009. Half for a degree in a related subject in which courses in neu-of the curriculum is made up of courses in physics and roinformatics form a small component of the degree. Toapplied mathematics. In the other half there are (i) cours- give one example, a survey of neuroinformatics teachinges in cell biology, neurobiology and psychology together in the UK in 2006 revealed that 23 universities offeredwith (ii) a variety of elective courses including neural such courses, mainly in the final year of study. These werenetworks, statistical inference and programming. In ad- in degree programmes in mathematics, physics, comput-dition, there is (iii) significant practical training in EEG ac- er science, informatics, electronics, engineering, bioengi-quisition and analysis. neering, biosciences, physiology, neuroscience, psychology or cognitive sciences.A1.2 Neuroinformatics as a significant part of adegree programme A2 Group 2 (Masters students)The Center for Neural Science at New York University, The definition of a Masters courses used here is that it is aUSA, offers a major in Neural Systems. In one half of the separate degree course taken after the Bachelor’s and hascourse, students study physics, chemistry, psychology as prerequisite the Bachelor’s degree. PhD courses thatand mathematics. In the other half, there are mandatory contain a large amount of course work where Masters de-courses on cellular & molecular neuroscience and on be- grees can be awarded to students who finish prematurelyhavioral & integrative neuroscience. The several elective are included in Section A3 (Group 3, PhD students).courses include computational neuroscience. There aretwo lab rotations. A2.1 Dedicated Masters degrees in neuroinformat- icsThe Radboud University Nijmegen, Netherlands, offers There are Masters degree programmes devoted specifi-undergraduate students in biomedical sciences a Master cally to neuroinformatics, or to one strand of neuroinfor-in Clinical Human Movement Sciences with an optional matics. Most of these courses are a combination of taughtMinor in Neuroscience. The latter comprises several sys- modules and a research project.tems neuroscience courses with a strong computationalcomponent and an elective of at least 4 months, which The goals of the 18-month Master in Neural Systems andmay be done in a relevant “wet” or computational lab. Computation at the University of Zurich and the Swiss Federal Institute of Technology is to supply training inThe Centre for Neurogenomics and Cognitive Research experimental, theoretical and computational neurosci-(CNCR) at the VU University Amsterdam, Netherlands, ences and neuromorphic engineering. The programmeoffers undergraduate neuroscience courses including is open to students with a Bachelor’s degree in biology,courses on computational neuroscience, neuroscience- chemistry, mathematics, physics, computer science, in-oriented bioinformatics and systems neuroscience. formation technology or engineering.The Faculty of Information Technology at the Peter The University of Manchester, UK, offers a 1-year MSc inPazmany Catholic University at Budapest teaches a 3-year Computational Neuroscience and Neuroinformatics to12

both biology graduates and those from the numerate sci- matics related topics, such as computational neurosci-ences. The first of three semesters has courses on compu- ence, neural development, systems biology, cognitivetational neuroscience and methods in neuroinformatics, modelling, data analysis and image analysis. The univer-together with a course in mathematics for the biologists sities offering these courses are Amsterdam, Groningen,and one in neuroscience for those from the numerate sci- Maastricht, Nijmegen, Rotterdam, Utrecht, and the VUences. In each of semesters 2 and 3, the students carry University of Amsterdam.out a research project, on two different topics. Fundedplaces are available. In Germany, the Universities of Bremen, Göttingen, Heidelberg, Magdeburg, Munich, Rostock and TübingenThe University of Plymouth, UK, offers a 1-year MSc in The- all now offer Masters courses in Neuroscience with a neu-oretical and Computational Neuroscience. Two teaching roinformatics component. Typically the courses are 18streams are recognised, according to whether students months long, combining taught courses, lab rotations,are from the life sciences or the physical sciences. Stu- and a research project.dents are taught a wide range of theoretical techniques,including mathematical and computational modelling, In addition, Germany still maintains, at a few places, theprobabilistic methods for analysing data and topics from traditional Diploma degree education in which studentsneuromorphic engineering and brain inspired comput- acquire a Diploma degree in Biology with a possible spe-ing. There are two semesters of taught courses and in the cialisation in neuroinformatics according to the coursesthird semester a research project is undertaken. they choose and the specialization in their research to- wards the Diploma thesis. In Freiburg the Diploma courseThe University of Edinburgh, UK, runs a large 1-year MSc is soon to be replaced by BSc and MSc programmes.degree programme in Informatics, comprising taughtcourses and a summer project. Students choose a par- The neuroinformatics-related specializations at Freiburg,ticular combination of courses. One of these is neuroin- Göttingen and Munich are in association with the Bern-formatics, with courses on neural computing, neural stein Centers for Computational Neuroscience (BCCN; seeinformation processing, computational neuroscience of Section A3.1).vision, cognitive modelling, probabilistic modelling and The University of Sheffield, UK, offers a 1-year MSc in Cog-machine learning. nitive and Computational Neuroscience.In Berlin, Germany, a 2 year Masters in Computational The Norwegian University of Science and Technology atNeuroscience started in September 2006. “It uses theo- Trondheim offers a 2-year Masters programme in Neu-retical approaches from a variety of disciplines including roscience, which has some neuroinformatics contentmathematics, physics, computer science and engineer- (http://www.ntnu.no/studier/helsefag/mnevro).ing to understand the brain”. The first year is devoted totaught courses, the second year to lab rotations and a re- The University of Helsinki, Finland is offering a 2-yearsearch project. The course is taught by the Berlin BCCN, Masters course in Neuroscience from September 2008.with representation from the three major universities in This comprises taught courses and a research projectBerlin. (consisting of one third of the total time). The focus is on experimental neuroscience although a few of the coursesA2.2 Courses as part of a Masters degree in an- are devoted to topics in neuroinformatics.other subject Courses taught in a physical sciences departmentAs for Group 1, a variety of courses with neuroinformaticscontent can be taken as part of a Masters degree course In the UK, both the 1-year Advanced Computing MSc atin another subject. These subjects may be either one of Bristol and the 1-year Bioengineering MSc at Imperialthe physical or the life sciences. College London have a neuroinformatics component.Courses taught in a life sciences department One variant of this theme is used at the University of Wa- terloo, Canada. The Centre for Theoretical NeuroscienceMany of the seven two-year Masters courses in Neurosci- (http://ctn.uwaterloo.ca) offers a diploma to students al-ence in the Netherlands include courses on neuroinfor- 13

ready registered for a Masters (or PhD) in a related disci- and mathematics. Students acquire theoretical and ex-pline. Students attend a course on simulating biological perimental expertise in neurobiology and psychologysystems, two courses chosen from a list of options and a (including information processing in nerve cells), phys-seminar in theoretical neuroscience. ics (including neural networks and statistical mechanics) and computer science (including computation theoryThe International Masters Programme in Computational and optimization).and Systems Biology in Stockholm, Sweden has a mod-ule on mathematical modelling that focusses on neural The Gatsby Computational Neuroscience Unit at Uni-modelling. http://www.csc.kth.se/utbildning/program/ versity College, London, UK has run, since 1998, a 4-yearcompsysbio/. PhD programme in theoretical and computational neuroscience and machine learning. In the first year, there isThe Master of Science programme in Computational intensive instruction in techniques and research in theo-Biology at the Norwegian University of Life Sciences, retical neuroscience and machine learning. This is madeAas, Norway also has a neuroinformatics component. up of core courses followed by specialist courses in theo-http://www.umb.no/21220 retical neuroscience and in machine learning and then a research project. Students have to undergo assessmentA3 Group 3 (PhD students) before admission to the 3-year research for their PhDs.Most students in neuroinformatics have to acquire sev- The Doctoral Training Centre in Neuroinformatics anderal different types of knowledge and skills which should Computational Neuroscience at Edinburgh, UK, openednecessitate their attending formal training courses. In in 2002 and admits around 10 funded students per yearsome cases this training is integrated in the PhD course; on a 4-year programme. This is intended for studentsin some cases students receive their training while be- from the physical sciences and so a criterion for admis-ing enrolled in a programme in one of the related larger sion is a good level of mathematical and computationaldisciplines (e.g., physics, biology, computer science); in knowledge. The first year is effectively a Masters courseother cases, they attend short courses; in some cases, the involving a combination of coursework and research proj-training that they receive is acquired implicitly while car- ect. The first semester is shared with students studyingrying out their research project, without participation in for the MSc in Neuroscience. In the second semester, stu-formal courses. dents study neuroinformatics courses including a courseA3.1 Neuroinformatics PhD courses based on the local neuroinformatics research. Over the summer, students carry out a research project in an ex-The basic structure for training doctoral students in the perimental lab. During this first year, the students decideUSA would seem ideal for interdisciplinary education as on their PhD project, which they carry out in years 2 to 4.they study for over 5 years, with taught coursework inthe first two years (roughly equivalent to a Masters pro- In Germany, all four Bernstein Centres, at Berlin, Freiburg,gramme), followed by a research project (similar to a Eu- Göttingen and Munich offer training for PhD studentsropean PhD). in computational neuroscience. The courses offered by BCCN Berlin are formalised into a 3-year programme, inPhD programmes specialising in computational neuro- which, in addition to carrying out research, each PhD stu-science exist at the Universities of Chicago, Princeton, dent takes one full-time semester of course work.Pennsylvania and Carnegie Mellon. A3.2 PhD courses with a major neuroinformaticsThe Interdisciplinary Center for Neural Computation component(ICNC; http://icnc.huji.ac.il) at the Hebrew University, Je-rusalem, Israel, is the largest and oldest dedicated neu- The Computation and Neural Systems programme atroinformatics PhD programme worldwide and has been Caltech, USA, combines the study of computation within existence since 1992. It takes in around 12 funded stu- that of neural systems. The curriculum is designed to pro-dents per year for a 5-year course in computational neu- mote a broad knowledge of relevant aspects of experi-roscience. Student backgrounds include biology, physics, mental and theoretical molecular, cellular, neural, andchemistry, psychology, computer science, engineering systems biology; computational devices; information14

theory; emergent or collective systems; modelling; and A3.3.1 Short courses with a duration of one week orcomplex systems. moreAt Weill Cornell, USA, neuroinformatics graduate training These courses combine seminars with hands-on, practi-is part of a larger programme in computational biology. cal work and are restricted to a small number of students,The course is made up of one summer of lab rotations, typically between 12 and 30. Course fees are charged butone year of coursework in mathematics, applied math- most courses award stipends to students.ematics, and computer science, a year of lab rotationsand biology coursework at the medical school campus, The courses are very competitive and are designed forand then thesis work (2-3 years). About one third of the early career researchers and most attendees are doctoralstudents are interested in neuroscience, and the students students. The courses fulfill the need for students in neu-with little biology background seem to benefit a lot from roinformatics who wish for training in another techniquethis training. or wish to increase their knowledge of a particular topic. However, they cannot serve to give a basic grounding inThe German Research School for Simulation Sciences has a subject (such as teaching neuroscience to a physicist).initiated a joint training activity involving RWTH Aachen Here are some examples of short courses:and the Jülich Research Centre (http://www.grs-sim.de/),hosting the largest civil computing resource in the world. The Marine Biology Laboratory, Woods Hole, USA (http://Masters and PhD degrees are awarded by the RWTH www.mbl.edu/) and Cold Spring Harbor, USA (http://Aachen after 2 and 3 years, respectively. www.cshl.edu/), each runs an annual programme of courses. The 3-week course Methods in ComputationalIn the Netherlands, CNCR at the VU University Amster- Neuroscience, the 2-week course Neuroinformatics (fo-dam offers PhD research projects on neuroinformatics cusing on methods for acquisition, storage and analysistopics. Students can attend courses in neuroscience as of time series neuroscience data and, more recently, com-well as from other disciplines such as mathematics and putational neuroanatomy), both offered by Woods Hole,theoretical biology. and the 3-week course Computational Neuroscience: Vi- sion offered by CSHL all emphasise the multidisciplinaryIn Japan, the Department of Bioinformatics and Genom- approach. Many other courses would be of interest toics, Nara Institute of Science and Technology, the Depart- students studying neuroinformatics, but generally arement of Complexity Science and Engineering, University less accessible owing to the severe competition for plac-of Tokyo and the Graduate School of Life Science and es with neuroscientists. About half the participants onSystems Engineering, Kyushu Institute of Technology all the Woods Hole courses are graduate students.offer teaching and research programmes in computa-tional neuroscience. The Computational Neuroscience Course at Okinawa, Japan has run annually since 2004. Currently it is threeA3.3 PhD training delivered through short courses weeks long. Its aim is “to provide opportunities for youngThere is a wealth of courses which PhD students can at- researchers with theoretical backgrounds to learn thetend, ranging from one-off single day (or even shorter) latest advances in neuroscience, and for those with ex-courses to week-long or month-long courses. Many run perimental backgrounds to have hands-on experience inon an annual basis. These courses are attended by PhD computational modelling.”students, postdoctoral researchers and, exceptionally, The 4-week European Advanced Course in Computa-academic staff. Therefore, the comments made in this tional Neuroscience This course has run every year sincesection about these courses may also apply to groups 1996, offering 30 places per year. The course is intended4 (Postdocs) and 5 (Academics), as well as to group 3. It for “advanced graduate students and postdoctoral fel-is convenient to distinguish short courses which are for lows who are interested in learning the essentials of theone week or more from those which are for less than one field.” The course offers a combination of lectures and tu-week. torials with small projects conceived by the students are performed by them under the guidance of course tutors and faculty. 15

The one-week school in April/May 2008 in St Petersburg, mathematicians and computational people, runs 2-hourRussia, Models in Neuroscience: Turning Experiments into tutorials in which neuroscience topics figure strongly.Knowledge (http://www.neuroscience.spb.ru/school) These are attended by pre- and postdoctoral workers andfocused on training students to transform experimental by academics.data into plausible theoretical models. The goal of theschool was to bridge the gap between future cellular and Various organisations, such as learned societies or localcognitive neuroscientists and to engage the students networks, run one-off courses teaching a technique. Formajoring in physics and mathematics into the field of example, the UK Spike Train Analysis Network (http://computational neuroscience. The course was designed www.spiketrain.org/) ran a one-day workshop for math-for graduate students and young post-doctoral research- ematicians on spike train analysis methods.ers with interest in cellular and cognitive neuroscience as Immediately following the 1st Neuroinformatics Con-well as the students with physics/math majors. gress, the INCF held a two-day autumn school for PhDThe week-long course on Computational Neuroscience students on methods for imaging cortical activity.run by the BCCN, Göttingen, Germany, has been present- The German Neuroscience Society supports a number ofed annually since September 2003. It combines 3-hour annual short neuroscience courses, amongst those beingtutorials by visiting speakers with the study of selected a 1-week course in Freiburg, on Analysis and Models inresearch papers. The course is intended as a tutorial for Neurophysiology.BCCN students as well as an open course for external stu-dents. It attracts around 25 participants. A4 Group 4 (postdoctoral researchers)A3.3.2 Short courses with a duration of up to one Many neuroinformatics practitioners enter at the post-week doctoral stage. These are mainly people who are educat- ed in one branch of science and who require training inThere is a variety of training events of this length, ranging another branch.from a few hours to a day or two. Some of these occurregularly, being attached to regular scientific meetings; A4.1 Fellowshipssome are organised on a one-off basis. Some are free and In 1994, the Sloan Foundation recognised that many neu-some charge a fee. Here are some examples: roinformaticians enter from the physical sciences. TheSince 2002 the functional neuroimaging community in- Foundation established the Sloan Centers for Theoreticalvolved in Statistical Parameter Mapping has held a vari- Neurobiology at five USA research institutions, Brandeis,ety of training events lasting 2-3 days typically, initially in Caltech, NYU, Salk Institute, and UCSF. The initial em-London and now spreading to other locations. The cours- phasis was on pre- and postdoctoral training. When thees are very popular. They are attended mainly by people Swartz Foundation took over the funding in 2003, havingworking in the field already and fees are charged. been co-sponsor from 2000 to 2003, this became princi- pally a postdoctoral programme.The Japanese Neural Network Society has organised aNeuroinformatics Summer/Automn School from 1999 to The current Sloan-Swartz programme offers 2-year fel-2003 and from 2006. lowships for both experimentally and theoretically trained scientists from the physical sciences to work inA 1-day techniques course precedes the annual Human experimental brain research laboratories. In this environ-Brain Mapping conference. ment, they become conversant with neuroscience ques- tions and experimental approaches in neurobiology,The Society for Neuroscience holds short courses at the enabling them to apply skills learned from studying theSfN annual meeting, such as the annual one-day course physical sciences to problems in neuroscience. There areon the widely used neural simulator, NEURON (http:// now 11 centres, Harvard, Princeton, Columbia, Yale, UCSDwww.neuron.yale.edu/dc2008.html). and Cold Spring Harbor having joined the original five.NIPS, the annual Neural Information Processing Systems These centres vary in their requirement for Sloan-SwartzConference (http://nips.cc), which attracts predominantly postdoctoral fellows to undergo formal training. The pro-16

gramme at Caltech is closely associated with the post- A5 Group 5 (Academic staff)graduate Computation and Neural Systems Programme There are no courses designed specifically for this group.(Section A3.1). It is very rare for them to attend the longest runningSeveral funding bodies offer fellowships for which aspir- short courses (never in the case of the annual Europeaning researchers at the postdoctoral level could apply. In course on computational neuroscience; occasionally forthe UK, the Medical Research Council offers Training Fel- Woods Hole courses). Such courses tend to be designedlowships in the areas of Computational Biology, Bioinfor- with the early career researcher in mind. Additionally,matics and Neuroinformatics. spending several weeks studying at a course may not be feasible for academics. However, most of the teachers atSeveral of the UK Research Councils offer discipline hop- the short courses are academic staff who benefit throughping grants to “enable established researchers in the interacting across the disciplines. Academics do attendengineering or physical sciences to apply for funding to short courses of a few days, particularly those attached toinvestigate and develop ideas, skills and collaborations in a larger event such as a conference. The number of aca-biological, clinical and population health research. Alter- demics who attend varies from course to course.natively, established life science researchers can apply forfunding to develop ideas, skills and collaborations with From 2000 to 2003, Edinburgh University, UK, ran a one-physical scientists or engineers.” week summer school on training in the use of neural simulators, for around 30 students. Occasionally, academicUS National Research Council (NRC) will pay a bonus in staff attended as students and integrated well.salary (currently $10,000) for people with degrees in phys-ical sciences (physics, chemistry, mathematics, statistics) There are other types of extended events attended byor engineering who wish to do postdoctoral research academics which can have a training element. One ex-into biomedical sciences. This is to encourage people to ample of this is the 3-week neuromorphic engineeringcome into the field. This applies to neuroinformatics or workshop held annually at Telluride, USA. Similar shorterneuroscience. The NIH will also pay this bonus to people workshops have been initiated in Europe, made possiblewith these Ph.Ds to enter NIH Intramural programmes. by several EU-funded projects pooling their resources.Researchers holding postdoctoral fellowships who want The Brain Connectivity Workshop (www.hirnforschung.to develop skills in other disciplines can attend MSc net/bcw) has established itself as a successful venue forcourses (usually at their own cost). high-level discussions of all aspects of the structural, dynamical and functional organisation of the brain. It runsA4.2 Short courses for 2-3 days in spring every year in a different location.While the many of the attendees at the short courses In some years it is preceded by a short course bringingmentioned under in Section A3.1 are PhD students, a sig- newcomers up to speed with relevant concepts.nificant proportion (up to 50% in some cases) are post- Many academics attend the tutorials held in associationdoctoral researchers. with larger events, such as conferences.In addition, postdoctoral researchers acquire training in Members of academic staff are able to obtain financialspecific techniques through attending at courses of a few support occasionally from national or international fund-days or less. These short courses have been described ing organizations for learning techniques in a differentunder the provision for PhD students in Section A3.2 lab. Such fellowships are offered, for example, by DFGabove. (Heisenberg; Germany), Humboldt Foundation (Ger- many), Wellcome Trust, Royal Society (UK), NZ MRC, EU (Marie-Curie). 17

Appendix B: Links to Relevant Web (j) Other relevant web sites: The Society for Neuroscience‘s neuroscience teachingSites portalThe information about training provision here described http://www.ndgo.net/sfn/nerve/in Appendix A is a sample of what is available. More infor- The journal PLoS Computational Biology, prominent inmation is available on the Internet. Some relevant web- publishing in neuroinformatics, maintains an extensivesites have been mentioned in the text and some other section with tutorials, perspectives and informative se-are given below. Most of these carry information about ries such as “Ten simple rules for...”, “Getting started in...”,courses in a particular country or for particular types of “What has computational biology done for...”.students. There is no one web site with universal cover- http://www.ploscompbiol.org/age. At the workshop, it was agreed that such a resourcewould be very useful and one of the recommendations Site about the EC’s Bologna process:from the workshop was that the INCF facilitate the pro- http://ec.europa.eu/education/policies/educ/bolo-duction of a training portal (Recommendation R2). gna/bologna_en.htmlWeb sites about neuroinformatics training:(a) Masters programmes in the Netherlands: http://www.neurofederatie.nl/masters/(b) PhD programmes in computational neuroscience in the USA: http://neuroscienceblueprint.nih.gov/neurosci- ence_resources/training_comp_neurosci.htm(c) Masters and PhD neurosciences courses in Europe: http://fens.mdc-berlin.de/nens/(d) Masters and PhD courses in the Bernstein Network for Computational Neuroscience, Germany http://www.nncn.de/(e) Summer schools in neuroscience: http://www.bccn-berlin.de/graduate_programs/ important-web-links(f ) Courses at Woods Hole, USA: http://www.mbl.edu/(g) Courses at Cold Spring Harbor, USA: http://www.cshl.edu/(h) The Okinawa Computational Neuroscience Course, Japan: http://www/irp.oist.jp/ocnc/(i) Two web sites giving a variety of information about neuroinformatics: http://neurobot.bio.auth.gr http://www.hirnforschung.net/cneuro/18

Appendix C: Workshop ProgrammeJuly 23:14:00 - 14:15 Welcome and orientation (David Willshaw)14:15 - 16:00 Session I: “Training in neuroinformatics” -scientific presentations16:00 - 17:30 Session II: “Current provision of training in neuroinformatics” -discussion in small groups19:00 DinnerGary Egan Educational programmes and professional development challenges in neuroinformatics with case studies in neuroimagingMark Van Rossum Neuroinformatics and Computational NeuroscienceBarry Richmond Neuroinformatics and training from an experimentalist’s perspectiveJuly 24:09:00 - 13:00 Session III: “Future provision of training in neuroinformatics” -scientific presentation and discussion in small groups13:00 - 14:00 Lunch14:00 - 17:00 Session IV: “Mapping out the future” -work on draft report in small groups and discussion18:00 Reception hosted by the Edinburgh Doctoral Training Centre in Neuroinformatics and Com- putational NeuroscienceRolf Kötter Neuroinformatics training for the future - a personal viewJuly 25:09:00 - 12:00 Session V: “Formulating recommendations” -discussion in small groups12:00 - 13:00 Discussion and conclusions 19

INCF Secretariat, Karolinska Institutet, Nobels väg 15A,SE-171 77 Stockholm, SwedenTel: +46 8 524 87093 Fax: +46 8 524 871450Email: info@incf.org www.incf.org

Needs for Training in Neuroinformatics

by marina761 on Nov 26, 2010

Accessibility

Upload Details

Usage Rights

Statistics

Needs for Training in Neuroinformatics Document Transcript