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(0%QHW7KH*OREDO%LRLQIRUPDWLFV Data Processing and Integration 5” conference and Management Committee meeting; a full- 1HWZRUNLQ$6LOYHU$QQLYHUVDU\ day EMBnet workshop; and finally, the business meeting itself. Here, we review the motivation for the EMBnet workshop, and present its main con- clusions. Background EMBnet’s 2013 AGM was a significant event, mark- ing the 25th anniversary since its foundation (in 1988), making it the oldest, widest network in the world. However, notwithstanding Teresa K Attwood EMBnet’s history and substantial contributions to , Manchester, United the field of bioinformatics during the past three Kingdom decades ( e.g ., see Attwood et al ., 2011), in 2010, the Executive Board 6 set out a vision for a new EMBnet, one that would allow it to evolve more Received Published 18 March 2013; 19 August 2013 effectively as a global organisation. Amongst its Summary key recommendations, the Executive Board sug- EMBnet’s 2013 Annual General Meeting (AGM) gested that there was an urgent need to: and associated events were hosted in the TRYP 1. review, streamline and clarify EMBnet’s current Valencia Oceanic Hotel, Valencia, Spain, from membership scheme; 14 to 18 May. The AGM, the silver anniversary 2. review how EMBnet might form strategic alli- of EMBnet’s foundation, provided a timely op- ances with other bioinformatics networks and portunity both to review our progress since the organisations; “EMBnet Moving Forward: 2010 & beyond ” work- 3. consider how it might compete more strategi- shop hosted in Ruvo di Puglia, Italy (Attwood et cally in global funding calls; al ., 2010), and to showcase the work of our al- 4. review the evolving role and internal structure lied SeqAhead project. EMBnet has undergone of EMBnet.journal , and consider more tacti- significant changes since 2010: it has rebranded cal publishing strategies; and, in light of these and launched a new website; it has formed new considerations, alliances; it has incubated new initiatives (notably, 5. review and revamp EMBnet’s current name, GOBLET 1: (Global Organisation for Bioinformatics brand and website. Learning, Education & Training) and multidiscipli- Ultimately, we wished to strengthen EMBnet’s nary research projects (namely, SeqAhead 2 and foundations, to create a competent, valuable AllBio 3); and it has formally introduced structural and focused organisation, both to complement changes to streamline our activities and broaden existing and emerging bioinformatics institutes, our membership. networks, associations and societies worldwide, The events allied to the AGM included a full- and to maintain EMBnet’s relevance in 2010 and day EMBnet hands-on tutorial 4 on “RNA-seq and beyond (Attwood et al ., 2010). Our goal was to ChIP-seq data analysis”, given by Endre Barta better define EMBnet’s role in European and glob- (U. of Debrecen, Hungary) and Eija Korpelainen al contexts, and open new avenues via which the (CSC- IT Center for Science, Finland), and on organisation could move forward, for the benefit “NGS and structural Biology”, given by Goran of its global membership. Neshich (EMBRAPA, Brazil), Jose R. Valverde (CNB- The 2013 AGM, EMBnet’s silver anniversary, was CSIC, Spain) and Gert Vriend (CMBI, Holland); the thus an opportune moment to reflect on how far two-day SeqAhead “ The Next NGS Challenge: we’d progressed towards meeting the 2010 rec- ommendations. 1 http://www.mygoblet.org/ 2 http://www.seqahead.eu/ 3 http://www.allbioinformatics.eu/doku.php 4 http://www.thenextngschallenge.org/index.php/pro- 5 http://www.thenextngschallenge.org/ gram/ngs-workshop 6 http://www.embnet.org/about/executive-board (0%QHW MRXUQDO 19.1 REPORTS 17

Update on Achievements Improving the EMBnet brand & promoting our activities more effectively A taskforce had been set up to consider how to improve EMBnet’s brand and Web presence. Working closely with the Publicity and Public Relations Project Committee 7 (P&PR PC), a new logo was introduced, together with the strapline, “Bioinformatics without borders ”, attempting to encapsulate EMBnet’s global mission more ef- fectively. The challenging task of designing a new Figure 1. Screen capture showing the new EMBnet website, website was also commenced. After exploring logo and strapline. several design prototypes, we engaged Itico (a non-profit Private Limited Company supporting perimented with a new Web-based publication, the iAnn project) to implement the ideas – see so-called EMBnet.digest (Figure 2, middle pane), Figure 1. Although the website is still undergoing to try to give a flavour of EMBnet’s activities and revisions, it’s gratifying to know that it has already upcoming events on a more regular (monthly) attracted some positive feedback from the com- basis. As this appeared to be a popular mecha- munity via Twitter. nism for disseminating news, the P&PR PC subse- In parallel with these developments, we had quently overtook its production, and also created also proceeded to evolve the highly success- a new ‘look & feel’ (Figure 2, right-hand pane). ful EMBnet.news 8 into a peer-reviewed journal – During the last 18 months in particular, the EMBnet.journal 9 (Figure 2, left-hand pane). The Executive Board also worked closely with the P&PR additional time taken to produce peer-reviewed PC to establish sponsorship/patronage agree- issues, however, left a gap in our ability to make ments to promote the work of EMBnet more wide- timely news announcements. We therefore ex- ly, mostly notably at ISCB Latin America 2012 10

Figure 2. From left to right, screen-captures showing the previous cover of EMBnet.journal , the original ‘look & feel’ of EMBnet. digest, and the current re-designed digest.

7 http://www.embnet.org/about/publicity-public-relations 8 http://journal.embnet.org/index.php/embnetnews/issue/ archive 9 http://journal.embnet.org/index.php/embnetjournal/in- dex 10 http://www.iscb.org/iscb-latinamerica2012 18 REPORTS (0%QHW MRXUQDO 19.1

Figure 3. The B 3CB kick-off meeting that launched GOBLET.

(Chile), BITS 2012 11 (Italy), NETTAB 2012 12 (Italy) and Figure 3. The participants concluded that, build- ISCB Africa ASBCB 2013 13 . ing on the achievements of the Bioinformatics Training Network (Schneider et al ., 2012), a Securing strategic alliances with other organi- Global Organisation for Bioinformatics Learning, sations Education and Training (GOBLET) was needed Two very significant alliances have been formed to coordinate world-wide bioinformatics training since 2010, both related to EMBnet’s commitment activities: to share, not duplicate, effort; to share, to bioinformatics training. First, having become a not duplicate, cost; to work together in a mutually formal affiliate of ISCB, a press release was made respectful way towards common solutions and a announcing the intention of the ISCB and EMBnet sustainable future. To this end, a Memorandum to collaborate on bioinformatics education and of Understanding (MoU) was drawn up to estab- training ( ISCB press release 14 , 2011). This will ensure lish GOBLET as a legally registered foundation, that, whenever possible, EMBnet training courses following the successful model of EMBnet. Since are incorporated into ISCB meetings, especially the ten founding members (EMBnet, ISCB, ASBCB, those in developing regions. Importantly, the col- ISB, SoIBio, APBioNet, BTN, SeqAhead, NBIC and laboration also establishes a framework for foster- EBI) signed the MoU, 16 further organisations have ing future EMBnet and ISCB Student Council ac- pledged their commitment to formally create tivities for the benefit of the global bioinformatics and support the GOBLET Foundation 15 . community. The second alliance was extremely ambitious. Competing for funds for some of our activities A small workshop was held during the 2012 AGM Since 2010, two important research projects have in Uppsala, Sweden, at which representatives also been incubated and funded, both relating from nine other Bioinformatics, Biotechnology, to EMBnet’s involvement in NGS activities. First was and Computational Biology (B3CB) the Next Generation Sequencing Data Analysis societies, networks and projects came together Network (SeqAhead) COST Action (BM1006), the to discuss the need for a more holistic view of kick-off meeting for which took place in Brussels, bioinformatics training across the globe – see Belgium in March 2011. By establishing a strong European network of NGS, data-analysis and in- 11 http://bits2012.dmi.unict.it/conferencevenue.html formatics centres, SeqAhead aims to facilitate 12 http://www.nettab.org/2012 / 13 http://www.iscb.org/iscbafrica2013 and stimulate the exchange of data, protocols, 14 http://journal.embnet.org/index.php/embnetjournal/arti- cle/view/217/459 15 www.mygoblet.org (0%QHW MRXUQDO 19.1 REPORTS 19

Figure 4. From left to right, SeqAhead’s first scientific meeting and AllBio’s kick-off meeting. software, experiences, ideas and, crucially, train- Node re-elections, as member status will relate ing. Erik Bongcam-Rudloff is the grant-holder and strictly to the payment of the annual subscrip- project Chair, and Terri Attwood the project Vice tion fee. In addition, the new statutes oblige Chair; Andreas Gisel leads Work Group (WG) 2, the Executive Board (EB) to work more closely which is developing an action plan for NGS bio- with Project Committee (PC) Chairs, via a formal informatics; Eija Korpelainen leads WG 3, which Operational Board (OB), and allow the PC Chairs concerns the design and implementation of soft- greater flexibility to recruit enthusiastic members ware for NGS data analysis; and Gert Vriend leads to help with their activities. Overall, these changes WG 5, which coordinates the project’s dissemina- should allow future AGMs to run more efficiently: tion, education and training activities ( www.seqa- e.g ., elections will only be held for members of head.eu ) – see Figure 4 (left-hand pane). the EB and PC Chairs (committee members will The second success came in the form of the not require election); and there will be less obliga- EU Coordination Action, AllBio, which aims to tory reporting, and hence more time for discus- broaden the bioinformatics infrastructure to uni- sion and action! cellular, animal and plant science. The kick-off The new statutes were finally ratified in April meeting was also held in Brussels, in November 2013. Since then, we’ve welcomed one new or- 2011 – Figure 4 (right-hand pane). Once again, ganisational member – The Genome Analysis Erik Bongcam-Rudloff coordinates the project, Centre (TGAC), Norwich, UK, represented by Vicky and partners include Andreas Gisel, Terri Attwood, Schneider – and several new individual mem- Eija Korpelainen, Gert Vriend and Laurent Falquet bers. (www.allbioinformatics.eu ). The 2013 AGM workshop Structural changes Taking advantage of the new statutes, and the Arguably, the most significant development since greater time afforded for discussion, the 2013 2010 was the consent, during the 2012 AGM, to AGM was preceded by a workshop (see Figure 5). radical revisions of EMBnet’s statutes and byel- This was organised into four main sessions, focus- aws, in order both to streamline how we conduct ing on issues relating to i) membership fees and aspects of our business (especially our election sponsorship; ii) the website, EMBnet.digest , social processes) and, for the first time, to allow admis- networking and QuickGuides; iii) EMBnet.journal sion of individual members. and fund-raising; and iv) video-conferencing and To this end, we removed the requirement for future priorities. The first two of these sessions were government mandates, and implemented an run as parallel break-out groups, followed by ple- online payment system, allowing new members nary reportage; the remaining two were run as (both individual and organisational) to join more general group discussions. There were also sev- efficiently. Accordingly, EMBnet will no longer eral ‘sticky-note’ exercises, to encourage partici- have National Nodes, although we will continue pants to think ‘on the hoof’ about a range of im- to recognise those Nodes that have National sta- portant topics, including potential future Editorial tus; and there will no longer be a requirement for Board members for EMBnet.journal ; additional 20 REPORTS (0%QHW MRXUQDO 19.1

students (see next section). Another valuable sug- gestion was that we could explore the idea of joining student membership with the ISCB. Sponsorship In recent years, EMBnet has been approached by several organisations seeking sponsorship, patronage or endorsement of their events. While there is much to be gained by promoting EMBnet’s activities in this way, nevertheless, a policy and an appropriate budget would need to be in place in order for us to be able to respond efficiently and consistently to requests of this type. Figure 5. Participants of the 2013 AGM workshop. The questions for the group therefore con- cerned the types of event we should sponsor, the pages, sections and/or functionalities that could level of annual budget that could be set aside to be included in the new website; potential sources support these or other strategic events (in terms of funding; and EMBnet’s future missions and pri- of visibility, to prompt new alliances, collabora- orities. The main outcomes of the discussions and tions, and so on), and what forms of sponsorship exercises are reviewed below. EMBnet might be able to provide. There was general consensus that EMBnet Membership fees should sponsor a range of events (not just those In previous meetings, the OB had discussed the planned by networks/societies/organisations with possibility of changing EMBnet’s fee structure: for whom EMBnet already has special agreements), organisations, the proposal was to drop the fee but preferably those in which mutual benefits from €1,000 per annum to €500; for individuals, are apparent. The kinds of sponsorship offered the proposal was to introduce a fee of €50. by EMBnet could include keynote speakers at We wished to use this opportunity to explore meetings, or trainers at courses, tutorials and so with the full EMBnet Board whether the propos- on; travel bursaries for students; and conference als were optimal, what might be their pros and gadgets. It was proposed that we should set cons, and whether there were alternative models aside between 10 and 15% of EMBnet’s annual that we could adopt. We also wished to consider surplus in order to be able to respond to future whether we could offer any new membership sponsorship requests. benefits, and, where new proposals had been made, what might be their associated benefits. Website, EMBnet.digest and Social Networking The discussions on this topic were surpris- The new website had been up and running for a ingly congruent: all groups agreed that a hybrid while, but the migration of content from the previ- model of fees would be optimal, in which some ous site had been an enormous task, and many organisations would be able to pay an annual aspects remained to be resolved. Perhaps more fee of €1,000 and others €500, while individuals importantly, the burden of maintenance was would pay €50, or €15 if they were students (but falling to one or two individuals alone. Help was the student rate would apply, say, for only three clearly needed to progress some aspects of the years for any individual, without supporting docu- site: these included the addition of EMBnet news mentation). and events; updating contents with new activities, The principal benefit for organisations pay- new projects, additional resources, etc .; adding ing €1,000 would be that their travel to the AGM and updating member details; maintaining the would be reimbursed (up to a ceiling of €500). mailing lists, and so on. In terms of additional benefits of EMBnet mem- During the workshop, a little time was spent re- bership that could potentially be added to the viewing the website, and demonstrating the ease website, several suggestions were made: these with which all members can login to the system, included opportunities to share facilities; to host upload news and events, and generally man- visiting staff or students; to access a list of train- age, and take responsibility for, their own content. ers; and the possibility to provide sponsorship for Overall, participants seemed very happy with (0%QHW MRXUQDO 19.1 REPORTS 21 the new site. However, it was recommended to EMBnet.journal reconsider the rotating banner, which was caus- The transition from the highly successful EMBnet. ing problems in countries where bandwidth is a news to the new, peer-reviewed EMBnet.journal problem. Another key recommendation was to has been a major challenge. While several sup- explore how to adopt a more unified image for plements containing conference abstracts have promoting EMBnet via member websites. All such been published, the main journal issues have feedback will allow us to build on the site and been much more difficult to produce. Therefore, generally improve the image that EMBnet pro- the discussions on EMBnet.journal focused pri- jects to the world. marily on how it could attract more research The ‘look and feel’, and management of articles and/or other content, and whether the EMBnet.digest were also discussed. Here again, journal should accept advertisements, in order to most of the work falls to one or two individuals, bolster its income. and help is needed to collate information more It’s clear that the principal problem facing the efficiently. The principal outcome of the discus- journal is lack of dedicated manpower. All agreed sions was that we should consider adopting a that hiring a paid, part-time assistant would be more exciting ‘look and feel’, which could be helpful, and that a small part of EMBnet’s surplus prototyped in the coming months. Moreover, a should be set aside annually to achieve this. schedule of ‘In focus’ contributions was agreed Several other conclusions were reached: first, that from now until October 2013, commencing with all members of EMBnet should provide a ‘good’ a focus on the AGM in the May issue. article, or perhaps encourage a student in their There was also a general discussion around group to submit some of their work; second, that the presence of EMBnet on social networks (via the journal could include a new ‘book review’ media such as LinkedIn, ResearchGate, Twitter, section; third, that the journal should include a Facebook, Wikipedia, etc .). EMBnet already has section dedicated to the Node ‘InFocus’ pages a successful LinkedIn site and a Wikipedia en- of EMBnet.digest , highlighting the special events, try. Given that EMBnet doesn’t have resource to activities and/or initiatives of EMBnet’s Nodes and dedicate to all such activities, it was suggested members; and finally, that we should explore that the website could be made ‘social media what models other journals adopt with regard to friendly’, to allow news, events, features and so on the inclusion of advertisements. to be exported to relevant social media, as and Fund-raising when appropriate, more easily. Fund-raising is an important activity for augment- QuickGuides ing EMBnet’s finances and for galvanising its work QuickGuides 16 have been a long-standing and – without dedicated funds, it is much harder al- useful output of EMBnet. However, maintaining or ways to rely on the good will and dedication of updating them, and writing new ones, requires particular individuals. This discussion therefore commitment and effort. As many of the Guides centred on what types of activity EMBnet should had not been updated and no new Guides had seek to get funded, and what funding opportuni- been created for several years, the question was ties might be available to support them. whether we should keep them. There was general agreement that the types In the discussion that followed, all agreed of activity that EMBnet would like to be in a posi- that we should maintain EMBnet’s portfolio of tion to fund, or offers it would like to be in a po- QuickGuides, and that these should be peer-re- sition to make, would include travel fellowships viewed in order to maintain quality. Two comple- for students; support for EMBnet speakers and/or mentary models for managing the Guides were trainers; administrative support for EMBnet.journal ; proposed: i) that they should be made available EMBnet events (tutorials, workshops, conferences, via the GOBLET website, as part of its educational/ etc .); and joint research projects. training content; and ii) that they should be man- The first, most obvious, mechanism by which aged via the Open Journal System (OJS). As these to enable such activities and benefits was to in- models are not mutually exclusive, it would seem crease EMBnet’s membership. We are, of course, sensible to proceed with both! hopeful that the new, streamlined process for joining EMBnet, with is easy-to-use online pay- 16 http://www.embnet.org/embnet-quickguides ment system, will help to widen our membership; 22 REPORTS (0%QHW MRXUQDO 19.1

Figure 6. Left-hand pane, a reward for Domenica D’Elia for sterling work as P&PR PC Chair; right-hand pane, a toast to Vicky Schneider, representative of new organisational member, TGAC. but clearly, we need to do more. It was recog- ficiency, destroys morale, and increasingly deters nised that we need to improve our publicity people from attending. and outreach activities, and that we could and In consequence, it was agreed that EMBnet should be doing a lot more both to attract stu- will conduct an experiment to test around a doz- dent members and to give them visibility within en video-conferencing packages. Participants in EMBnet. Other ideas included merchandising the experiment would need to confirm their com- (e.g ., EMBnet T-shirts!), advertisements in the jour- mitment after the AGM, a protocol for conduct- nal, and possibly attracting donations (which are ing the experiment would be agreed during the within our statutes to receive). We should also be summer, and global testing would commence proactively consulting development agencies towards the beginning of the autumn. Ultimately, (UNESCO, etc .) and seeking joint research projects this should provide the optimal solution for all in- via national and international funding bodies. volved, and the results would be made available as a publication in EMBnet.journal . Video conferencing Maintaining the momentum of EMBnet’s activities Future priorities between AGMs is always a challenge, a chal- In thinking about the future of EMBnet, it has been lenge that rests with the PC Chairs and EB to ad- imperative to reflect on the impact of globalisa- dress. At one time, it was possible to hold interim tion on our once-European organisation, and to Committee meetings, Executive meetings and better define EMBnet’s role in the global bioinfor- meetings of the full Board using a (commercial) matics landscape. As EMBnet has evolved, so too online conferencing system called Marratech. has its mission and its priorities. Accordingly, the However, the company was taken over, the soft- question was what EMBnet’s missions and priori- ware was suddenly no longer available, and we ties should now be, and what we should be doing were obliged to find a new solution. After several to help get us there. trials, most monthly meetings of the EB and OB In terms of missions, there was general con- have been conducted with Skype, but this con- sensus that to promote, “ Bioinformatics without tinues to cause problems for many participants. borders ” should be our primary goal. EMBnet This has become an issue, especially for the bi- should disseminate best practice in bioinformat- monthly meetings of the full Board, because a ics, promote bioinformatics capacity in all coun- great deal of time is wasted while people try (of- tries, share bioinformatics knowledge, and, cru- ten unsuccessfully) to connect: this prohibits ef- cially, incubate new initiatives ( e.g ., like GOBLET). (0%QHW MRXUQDO 19.1 REPORTS 23

EMBnet’s priorities were considered to be to a more innovative and ultimately more produc- champion education and training; to achieve tive organisation. In particular, we hope that oth- better PR and outreach; to improve the roll-out ers will take the lead of those who’ve shouldered and recognition of EMBnet.journal ; to make bet- so much of EMBnet’s work in recent years, and ter use of our website in order to share more with will join us in our efforts to make EMBnet the pre- our communities; to invest strategically in our ac- eminent bioinformatics network in the world. And tivities; and, wherever possible, to apply jointly for perhaps some of us may yet live to see EMBnet funds to help realise our research, training and celebrate its golden anniversary! networking objectives. Acknowledgements Conclusion We are indebted to Ana Alvarez and Ana Conesa It’s clear that EMBnet has come a long way in the for their considerable efforts with the local organi- last three years, largely thanks to the enormous sation, especially for their restaurant recommen- efforts of a handful of individuals. Thanks are es- dations, and overall, for providing such a com- pecially due to Lubos Klucar for his work in run- fortable and welcoming environment. ning EMBnet.journal ; to Erik Bongcam-Rudloff for coordinating the SeqAhead and AllBio projects, References and to Andreas Gisel, who helps him to keep Attwood TK, Bongcam-Rudloff E, Gisel A, de Villiers E (2010) EMBnet - the European Molecular Biology Network, Moving these projects on track; and finally, to Domenica forward: 2010 & beyond. EMBnet.journal 16 (1): 8-14. D’Elia for her indefatigable work as EMBnet’s most Attwood TK, Gisel A, Eriksson N-E, Bongcam-Rudloff E (2011) passionate and committed P&PR PC Chair – see Concepts, historical milestones and the central place Figure 6. of bioinformatics in modern biology: a European per- During the 2013 meeting, we were also fortu- spective. In: Bioinformatics - Trends and Methodologies , Mahdavi MA Ed., Intech Online Publishers, November nate to be able to celebrate the arrival of our lat- 2011, ISBN 978-953-307-282-1. est organisational member, The Genome Analysis ISCB Press Release (2011) ISCB and EMBnet to collaborate Centre 17 (TGAC), represented by Vicky Schneider, on bioinformatics education and training. EMBnet.journal who immediately stepped up to take on many 17 (1): 6. new tasks (Figure 6). Schneider MV, Walter P, Blatter MC, Watson J, Brazas MD, Rother K, Budd A, Via A, van Gelder CWG, Jacob J, The workshop and business meeting were Fernandes P, Nyronen T, De Las Rivas J, Blicher T, Loveland lively affairs, packed to the brim with activities, J, McDowall J, Jones P, Vaughan B, Lopez R, Attwood TK, and suggesting much work that’s still to be done. Brooksbank C (2012) Bioinformatics Training Network (BTN): A We therefore call on everyone’s ongoing support community resource for bioinformatics trainers. Briefings in Bioinformatics 13 (3): 383-389. doi: 10.1093/bib/bbr064 and collaboration to help us evolve EMBnet into

17 http://www.tgac.ac.uk