2016 EMBnet Annual General Meeting – Executive Board Report

Domenica D'Elia Emiliano Barreto Hernandez Lubos Klucar Erik Bongcam-Rudloff

Domenica D’Elia1, Emiliano Barreto Hernandez2, Lubos Klucar3, Erik Bongcam-Rudloff4

1 CNR, Institute for Biomedical Technologies, Bari, Italy; 2 Centro de Bioinformática, Instituto de Biotecnología - Universidad Nacional de Colombia, Bogotá, Colombia; 3 Institute of Molecular Biology, Slovak Academy of Sciences, Bratislava, Slovakia; 4 Swedish University of Agricultural Sciences, Uppsala, Sweden.

D’Elia et al. (2017) EMBnet.journal 22, e887 http://dx.doi.org/10.14806/ej.22.0.e887

Received 2 March 2017; Published 14 April 2017

Abstract

During the past year, the Executive Board (EB) held regular monthly meetings either via Skype or using Adobe Connect. These meetings were carried out with the Interim Board (IB), comprising members of the EB and Teresa Attwood and Etienne de Villiers. The IB was established during the 2015 Annual General Meeting (AGM) both to support the new EB in its first steps forward (as three of its members were new), and to help oversee implementation and delivery of the investment strategy. The EB also regularly invited Special Interest Group (SIG) Chairs to participate at EB-IB meetings. Additional monthly meetings open to the full EMBnet constituency were also convened. In this report, we provide a brief overview of activities and achievements from June 2015 to October 2016.

Introduction

The first EB-IB meeting was held on 1 July. Erik Bongcam-Rudloff was elected Chair, Domenica D’Elia Secretary, Emiliano Barreto Treasurer. The fourth member, Lubos Klucar, retained his pivotal role in the maintenance of EMBnet.journal (ENJ).

The first actions of the EB were related to the investment strategy approved during the 2015 AGM in Oeiras (PT). In particular, priority was given to the following:

  1. hiring an ENJ Editorial Assistant (EA) for one year to help the Executive Editorial Board (EEdB) in the daily management of editorial procedures, including contacts with authors and article copy editing;
  2. assigning three fellowships for:
    1. re-designing the ENJ website;
    2. upgrading and updating of ENJ Open Journal System (OJS);
    3. improving usability, style and content of EMBnet’s website;
  3. making a ring-fenced donation to GOBLET to hire an Educational Assistant for two years to develop jointly-branded materials. This proposal aimed to benefit EMBnet, by making its commitment to E&T and to GOBLET clear; and to benefit GOBLET, by boosting the Foundation’s income and helping to create tangible, branded products.
In addition, the EB has been working on a range of other tasks relating to the work of the SIGs, ENJ, the website, the Stitching bank account, membership, sponsorships, etc.

EMBnet.journal’s Editorial Assistant: commitments and achievements

The EB convened a joint meeting with the ENJ EEdB to agree procedures and deadlines for hiring an assistant. A call1 was prepared and launched at the beginning of August, with a 1 September deadline for submission of candidacies.

From seven candidates, three were selected, on the basis of their skills and expertise, for interview on 29 September. The ENJ EEdB unanimously converged on Antonio Santovito, who has proved to be a reliable, motivated and enthusiastic professional.

Antonio was officially hired at the beginning of October 2016 and immediately started work on the most urgent tasks. First was to repair hacker damage to ENJ, which resulted in the loss of almost all EMBnet.journal and EMBnet.news PDF and HTML galley files (i.e., all files not directly included in the SQL database). This problem affected the productivity of the journal and delayed Antonio’s work to develop a strategy to increase the number of published articles.

Nevertheless, his work was crucial for the recovery of ENJ’s archives and much more.

After several weeks (and thanks to the personal archives of Laurent Falquet, Matej Stano and Lubos Klucar), Lubos, Antonio and George Magklaras (Chair of the Technical Management SIG) were able to restore all public content and to make the ENJ archives available again.

Erik’s team set up a new backup strategy, eliminating the possibility of this kind of catastrophe in future. However, this did not prevent the occurrence of fake ENJ article comments (advertisements). The worst attack happened in November 2015, when several hundred fake comments appeared in article Web pages within a few days. The comments were removed, corresponding users accounts were disabled and captcha was implemented on both ‘user registration’ and ‘add comment’ pages. This almost completely halted the problem – only a few such comments have since appeared on the site; however, it cannot be completely eliminated if we want to keep the commenting feature available. Hence, for now, the only effective prevention is manual removal of fake comments by Lubos and Antonio.

Fortunately, the ENJ OJS installation hasn’t shown any major technical problems, although we are still running on an outdated version of the OJS (2.4.3.0, January 2014). To ensure our installation is robust and reliable, it is essential to update to the newest OJS release as soon as possible, and to make regular updates. At the same time, the server running the OJS must be protected by security measures.

Thanks to the professional support of Antonio, the EB was able to release, in the same period, a re-styled EMBnet leaflet and a short presentation, which were immediately used for EMBnet-sponsored events. The ENJ logo was re-designed, as well as the layout of the different ENJ article types. Lubos and Matej also contributed to this work.

The dissemination strategy elaborated by Antonio, and its implementation, brought increased visibility to EMBnet and to the ENJ, as shown in the statistics in Antonio’s activity report (see Santovito, 2016). From May 2016, he was also involved in the curation of the content (e.g., announcement of events and news) of EMBnet’s website, and in editorial work relating to the production of EMBnet.digest.

Prior to the AGM, Antonio expressed his willingness to restyle EMBnet’s website. This was a personal gift from him in recognition of the opportunity to work with EMBnet. The website will have a more modern design, in line with ENJ’s new look-and-feel, will conform to the latest Web-design standards, and will be accessible from mobile devices. The new website will be released in spring 2017, hopefully on a new server.

Overall, the investment in an EA has been extremely positive and fruitful. Thanks to Antonio’s work, we obtained professional dissemination products, implemented an effective dissemination strategy, and improved ENJ’s visibility on the Web. Moreover, thanks to his availability to work on tasks that were not included in his duties, such as re-designing the ENJ and EMBnet websites, we did not need to assign the other fellowships forecast in the investment strategy to accomplish these tasks.

The opportunity to renew the EA contract will be evaluated during the 2016 AGM. Technical issues relating to the management and security of the EMBnet and ENJ websites, and updating the OJS, have yet to be solved, and will also be discussed.

EMBnet/GOBLET ring-fenced donation and Educational Assistant

In biology, data integration is limited by the great number of available resources, their size and frequency of updates, their heterogeneity and distribution on different servers. Integration of these data can therefore be achieved only by adopting flexible and extensible tools. XML, Web Services (WSs) and Workflow Management Systems (WMSs) can support the creation and deployment of software able to automate data retrieval and analysis.

A WMS is able to design and create workflows, and to manage their execution. Its main components are i) a graphical interface for composing workflows, entering data and displaying different types of results; ii) an archive to store workflow descriptions, as well as results of executions and related traces; iii) a scheduler able to invoke services when needed; iv) a registry of available services; v) Application Programming Interfaces (APIs) for interoperating with services; and vi) a monitor tool to control workflow execution.

For this to happen, a ‘technology-savvy’ status must be achieved by providers and users. In this status, databases adhere to standards, and include semantic metadata; software is distributed on the network and can interoperate; and data-analysis procedures can be carried out on the network. A shared methodology for software development should also be adopted by developers and service providers. This could include i) XML schemas for creating shared data models; ii) XML-based languages for data storage and exchange; iii) WSs for software interoperability; iv) ontologies for WS discovery, selection and interoperation; and v) workflows for executing analysis processes.

EMBnet digest, sponsorships and organisation of AGM 2016

With the support of Teresa Attwood, Axel Thieffry (Chair of the P&PR SIG) and Antonio, the EB produced the monthly EMBnet.digest, including many of the InFocus articles, and disseminated information about their release via the mail list and LinkedIn, Twitter and Facebook social networks. Axel has reported positive access statistics.

The NETTAB & IB 2015 event was organised by Domenica, co-Chair of the event, alongside Paolo Romano (IRCCS San Martino IST, Geno (IT)), Ralf Hofestädt (University of Bielefeld (DE)) and Matthias Lange (IPK, Gatersleben (DE)). The event included six keynote lectures, original research scientific talks and poster sessions, and attracted more than 80 participants from diverse European countries.

As for sponsorship, during this last year, EMBnet sponsored two big bioinformatics events, the “Joint NETTAB 2015 International Workshop and Integrative Bioinformatics International Symposium/sup>”, held 14-16 October, 2015 in Bari (IT), and the “Fourth International Society for Computational Biology Latin America Bioinformatics Conference (ISCB-LA)3”, held 21-23 November 2016 in Buenos Aires (AR), which was co-organised with the Asociación Argentina de Bioinformática y Biología Computacional (A2B2C).

In association with the workshop, Domenica and Paolo also organised a “Two-Day Hands-on Tutorial” on cutting-edge methods and approaches to key issues in bioinformatics analysis of omics data. The tutorial took place on 12-13 October, and was hosted by the Department of Computer Science of the University of Bari and the INFN, which kindly provided the computational services and IT resources of ReCaS, a project financed by the Italian Ministry for Education, University and Research.

For this event, EMBnet granted 10 free tutorial registrations for young researchers and students attending the meeting. The tutorial consisted of full- and half-day parallel tracks on “Genome re-Sequencing for the Detection of Genomic Variations in Human Diseases” (full day), “Structural Bioinformatics in Drug Discovery” (half-day), “Pathway Commons and BioPAX” (half-day) and “Analysis of small RNA-Seq Data and Identification of microRNA controlled Pathways” (full-day). Experienced trainers were invited: Fabio Iannelli, from the FIRC Institute of Molecular Oncology, Milan (IT); Anna De Grassi, Professor at the University of Bari (IT); Pasqualina D’Ursi, from the CNR Institute of Biomedical Technologies of Milan (IT); Emek Demir, from the Sloan Kettering Institute, New York (USA); and Ioannis Vlachos, from the DIANA-Lab, Hellenic Pasteur Institute/Department of Computer & Communication Engineering, University of Thessaly (GR).

ISCB-LA aims to inspire and foster collaborations between regional scientists and students to advance research in bioinformatics and computational biology in Latin America. The request for sponsorship came from Ignacio E. Sánchez, representive of the Argentinian EMBnet centre (Universidad de Buenos Aires) and member of the organising and scientific committee. EMBnet will have an exposition space, where our banner and publicity materials will be shown and distributed to conference participants. Erik will attend the event as EMBnet’s representative, and will demonstrate the eBioKit (more details will be reported during the AGM). A report on the conference will be published in ENJ.

NETTAB & IB joint workshop 2015. A group photo taken during the tour in Bari’s downtown.

Figure 1. NETTAB & IB joint workshop 2015. A group photo taken during the tour in Bari’s downtown.

2016 EMBnet Annual General Meeting

A proposal to organise the 2016 EMBnet AGM in April 2016, in conjunction with the SolBio International Conference and Workshop 2016 “Bioinformatics and Computational Biology for Innovative Genomics”, was sent to the EB by Cesar Bonavides-Martinez and presented during the virtual general meeting held on 16 September 2015. Although the proposal was interesting, the EB declined the invitation owing to the costs, which were high relative to the need to honour the investments agreed during the 2015 AGM. Therefore, Erik and Hadrien Gourle helped to organise a two-day practical course on next-generation sequencing, on 22-23 April 2016, in collaboration with Ana Conesa, coordinator of the DEANN project.

In October 2015, the EB launched a survey among EMBnet members seeking preferences for the location of the 2016 AGM. 15 Organisational Members answered the survey. Most preferred a European country, where costs would be cheaper. In addition to the proposal from Mexico, Erik, Domenica and Pedro Fernandes submitted offers. The cheapest proposal was from Domenica, to hold the AGM in Rome in conjunction with the 2016 NETTAB workshop, in collaboration with ELIXIR-IT. The proposal included, as satellite events, an ELIXIR Hackathon (organised by Paolo and Rafael Jimenez) and an ELIXIR/GOBLET tutorial (organised by Allegra Via and Terri), to be held in parallel before the workshop; a special session on Education & Training in Bioinformatics was included in the main programme (also organised by Allegra and Terri). The EB-IB and Chairs of SIGs agreed on Domenica’s proposal.

In March 2016, the kick-off meeting of the CHARME COST Action took place in Brussels (BE); Erik and Domenica attended. Erik was elected vice-Chair and Grant Holder and Domenica Chair of WG4. The Management Committee (MC) established the 2016-2017 action plan. Domenica and Erik proposed the NETTAB-EMBnet workshop as an event co-organised with CHARME, owing to the match in scope and aims. The main focus of the workshop is “Reproducibility, standards and SOP in bioinfornatics”, and the event will represent an exceptional opportunity to present CHARME to a large and relevant audience of bioinformaticians from different organisations, institutions and European countries. The proposal was warmly supported by the CHARME MC, and the dates fixed on 25-26 October for the workshop, and 24 October for the satellite events (tutorial and hackathon). The EMBnet AGM will take place immediately after, 27-28 October 2016.

Acknowledgements

Despite the problems of the last year, relating to the bank account and the hack of ENJ, we are proud of the year’s achievements. Erik’s unshakable optimism gave us the energy to keep on going in these situations, without hesitation. We also thank T.K. Attwood and E. de Villier for their support, and P. Fernandes, A. Thieffry and A. Santovito for their valuable contributions.

References

  1. Attwood TK (2016) An Active Investment Strategy for EMBnet - AGM workshop report, Oeiras, June 2015. EMBnet.journal 21:e867. DOI: http://dx.doi.org/10.14806/ej.21.0.867
  2. Santovito A (2016) EMBnet AGM 2016: EMBnet.journal Editorial Assistant Activity Report. EMBnet.journal 22:e881. DOI: http://dx.doi.org/10.14806/ej.22.0.881

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