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Reinforcement of the centre for computational solutions in the life sciences

Final Report Summary - RECOMPSOLS (Reinforcement of the Centre for Computational Solutions in the Life Sciences)

Project objectives and execution

The primary objective of the project entitled RECOMPSOLS was to improve and reinforce the research capacities of the Centre for Computational Solutions in the Life Sciences (Compsols). The centre is a multidisciplinary collaborative research venture situated at the Ruder Boskovic Institute in Zagreb, Croatia. The activities of the centre range from bioinformatics of entire genomes to quantum-mechanical treatment of small model systems and include efforts focused on docking, proteomics, and mechanistic biochemistry.

We had proposed to achieve the reinforcement through several complementary measures. In order to sustainably increase the human resource level of the centre, we devised a dynamic recruitment initiative, whereby, rather than simply funding graduate students for the entirety of their studies, we aimed to introduce short-term fellowships to finance the unpredictable period between the completion of undergraduate studies and the potential procurement of long-term funding by, for example, the Croatian Ministry of Science, Education, and Sport (MSES).

In order to reinforce the material resources of the centre, we had proposed to purchase a state-of-the-art computer cluster, and associated ancillary equipment, and install it on site. Access was to be granted to all members of Compsols as well as selected individuals in our partner network.

To increase the integration of Compsols into the ERA, we proposed several activities with an international focus. In particular, we planned to organise two international workshops on the Adriatic Coast and a summer school in Zagreb aimed at bringing together the communities from the Western Balkan Countries (WBC) and Member States (MS), in our broad research area. At the same time, we envisaged a series of exchange visits with laboratories, also in the WBC and MS, designed to better educate WBC students by exposing them to high-level research environments early in their careers and to strengthen our own ties to the MS and WBC to reinforce our ability to perform high-quality cutting-edge research. This would enable us to increase the uptake of computational life science techniques in the WBC and improve our own integration into the ERA.

Work performed and end results

(i) The Dynamic recruitment initiative (DRI)

The idea behind the DRI was to find an effective and efficient way to combat the chronic brain drain that is evident in Croatia. A major factor contributing to the brain drain is the uncertain and unpredictable nature of the potentially lengthy waiting period between the time that a given student completes her undergraduate studies and the time she is granted an employment contract by the MSES (or alternative source) to begin doctoral studies. Our concept involved bridging finance to selected students to cover this waiting period and reduce the tendency for those students to abandon the local system in favour of more ordered labour markets in Western Europe and the United States (US).

The DRI proved itself to be an overwhelming success, far exceeding our initial expectations in terms of its effectiveness and impact. We helped a total of twelve students as opposed to the originally planned six. We secured alternate funding sources for all twelve of these students, ten of whom stayed in Croatia. Only four cases were somewhat problematic in that the solutions we found were less than completely ideal (including the two brain-drain casualties).

However, all four of these were a direct result of the moratorium on public employment, introduced by the Ministry of Science Education and Sport at the beginning of 2010. We sincerely hope that this moratorium will soon be lifted and that those students with uncertain futures will find themselves with more secure positions.

(ii) Infrastructural support

In order to reinforce our material resources of Compsols, we had included the purchase of a computer cluster into the RECOMPSOLS project. The initial phase of the purchase was performed through a public tender, with a contract for purchase, delivery, and assembly signed and finalised in mid 2007, while the expansion to the final form of the cluster was completed in December 2007.

In a similar manner to the DRI, the cluster purchase outstripped our expectations as the computing power of the final hardware configuration significantly exceeded our initial planning, once again providing enhanced impact of the E.C. contribution to the project. In brief, the final cluster ( consisted of a total of 56 processor cores with 124 Gb of memory and approximately three Tb of disk storage space.

The operating system was installed immediately after delivery. After careful system optimisation and configuration of the job-scheduling system, the required software was configured, which was greatly assisted by the employment of a technical assistant in mid 2007, through the RECOMPSOLS project. The cluster performed outstandingly for the duration of the project and, apart from external power failures, it continued to operate at its full capacity since its inauguration.

(iii) Exchange visits and associated training measures

An additional initiative conceived to increase the participation of Compsols, and indirectly the WBC in the ERA, as well as to increase the uptake of computational methodologies in the WBC, was a series of strategically timed exchange visits. In all cases, the visits were conceived to serve as training measures of one type or another. In first year, of the project, we received visits from Jack Leunissen from Wageningen University in the Netherlands, who gave several lectures as part of a practical bioinformatics course.

In the second year of project, several of the visits were combined into an intensive summer school that spanned the period from April to June 2008. This included professors from notable universities and institutes in Germany, Poland, Slovenia and the United Kingdom. The student reaction was very positive and we are very pleased with the level of uptake of the techniques presented into the students' own research.

In the third year of the project, we hosted follow-up visits from Professor Vlasta Bonacic-Koutecky, from the Humboldt University Berlin, Professor Juergen Eckert through the National Institute of Chemistry, Ljubljana, Slovenia, and Professor Milena Petkovic from the University of Belgrade, Serbia. Professor Leo Radom from the University of Sydney, Australia, who had been the postdoctoral host to two Compsols scientists also visited us as part of a European trip. Each of these visitors gave a seminar during the course of their visit, while the more intensive local courses in the third year were provided by our own senior Compsols staff.

In particular, the local courses were timed to overlap with the visits from three students from the University of Mostar, in Bosna and Herzegovina. We integrated these students into Compsols activities, including the second workshop. They are a key aspect of our endeavours to encourage the uptake of computational life science solution in the WBC.

In addition to these external visits, many of the students employed through the DRI, and some senior Compsols staff, participated in extended study stays abroad. Apart from the positive impact on local career development, these visits helped to strengthen our ties with the International School of Advanced Studies (SISSA) in Trieste, the University of Groningen, the Ludwig-Maximillians-University in Munich, the Humboldt University in Berlin, the Friedrich-Alexander-University in Erlangen-Nurnberg, the National Institute of Chemistry in Ljubljana, the University of Barcelona, and the University of Newcastle upon Tyne.

Overall, the exchange program was extremely successful. We reinforced the existing contacts and fostered new collaborations with scientists in the MS and WBC. We established a new contact network with scientists in Bosnia and Herzegovina and successfully trained graduate students working on their PhD theses. Several ongoing projects and applications emerged as a direct result of the RECOMPSOLS exchange program. These included approved bilateral projects with Slovenia and Serbia, an application to the Alexander von Humboldt foundation to consolidate the Munich connection, an application to the Unity Through Knowledge Fund involving the Humboldt University in Berlin and the participation in an application for a FP7-PEOPLE-2010-ITN (Marie Curie Initial Training Network), coordinated through the University of Newcastle upon Tyne.

(iv) Workshop organisation

As part of our strategy to become a focal point for the increased uptake of computational solutions in the life sciences in the WBC, and as our major dissemination events, we successfully organised two international conferences on the Adriatic Coast.

The first meeting, entitled the Second Opatija Meeting on Computational Solutions in the Life Sciences took place in Opatija, Croatia from 4 to 9 September 2007. Altogether 83 scientists registered for that meeting, of which 75 actually participated. The most numerous were scientists from Croatia (32), followed by Serbia (10), Germany (8), Slovenia (6), Romania (4), Switzerland (3), Macedonia, Kosovo, United Kingdom and the Netherlands (2 scientists from each) and Bosnia and Herzegovina, Bulgaria, Italy, Austria and Norway (1 scientist from each). Three participants from Albania registered, but were unable to attend. The participants spanned the range from diploma students (1), doctoral students (29), and postdoctoral fellows, to senior scientists. Among the participants were the vast majority of persons that we had indicated in our project proposal to be our key collaborators.

The second event, entitled the Third Adriatic Meeting on Computational Solutions in the Life Sciences, took place in Primosten, Croatia, from 1 to 5 September 2009. Altogether, 73 scientists participated in the meeting. The most numerous were scientists from Croatia (43), followed by Germany (4), Serbia, Slovenia, Bosnia and Herzegovina and Switzerland (3 scientists from each), Macedonia, Austria, Italy, Sweden and Australia (2 scientists from each), Kosovo, the United Kingdom, Spain and the Netherlands (1 scientist from each). Two participants from Albania initially registered, but were unable to attend. The participants covered the range from diploma students (3), doctoral students and postdoctoral fellows (almost 40 altogether) to senior scientists. Among the participants were many scientists that we had indicated in our project proposal to be our strategic collaborators.

Both conferences involved specific activities designed to make the sometimes daunting world of computational biology more accessible to the student population, especially those from the WBC. In Opatija, we held hands-on practial sessions where we guided the students through the actual mechanics involved in carry out the calculations. In Primosten, we changed the format slightly to more informal, tutorial style, presentations with the student populations able to ask questions both about the techniques in general and specifically about problems they were having in their own research.

Apart from the positive effect of nurturing a more close-knit WBC community in computational life sciences and allowing them to make important contacts with eminent scientists from the MS, the workshops also had the desired effect of increasing the visibility of the centre, both as a unit but also for the individuals who devoted their time and effort to organising the meetings. Indeed, several opportunities to deliver invited lectures at prominent international conferences can be considered a direct result of the success of workshops 1 and 2. Indeed the concept has been so well received in the regions that our partner scientists from the National Institute of Chemistry in Ljubljana have decided to continue the biennial series and we sincerely look forward to actively participating in the 2011 event.

Closing remarks

Overall, we feel that the RECOMPSOLS project was an outstanding success. All major objectives were achieved and the team involved in the implementation of the activities functioned very efficiently together. Indeed, due to a fortunate set of circumstance combined with lots of hard work, the impact of many of the activities undertaken turned out to far exceed expectations. The position of Compsols is very much reinforced. We will continue to strive to achieve positive results in the future, including enhanced participation in the European Research Area (ERA).