October 7th – 10th saw, for the first time, all fifteen ESRs, associated PhD students and post-docs as well as all of the supervisors from the ten TRAIN beneficiaries meet together for an intense four days of work and study. Quite an achievement considering everyone’s busy schedules and the last minute cancellation of the entire Sheffield team’s flights, requiring them to hurriedly find an alternative route. This time the hosts for the workshop were Prof Guillermo Velasco and the team from Facultad de Biologia at Universidad Contplentuse Madrid (UCM). Madrid provided some welcome autumn sunshine and a great selection of restaurants with some excellent food to sustain us through the four days of very hard work. Thanks to all who made it a success.
Day 1, 7th October
After brief introductions from Guillermo Velasco and Endre Kiss-Toth (Programme Coordinator) the first session of the day entailed a lively session of “speed dating” where the ESRs had to verbally brief listeners about the background and aims of their individual projects in just four minutes before moving round to do it again to someone new. This was a great way to focus on the essence of their work to date and learn how to distil the information into a concise and clear message. It also ensured a lively and noisy first 45 minutes of the day.
After this, it was straight into the first learning session of the day, which focussed on the essentials of prostate cancer. This was presented by five of the ESRs who are working on the cancer related aspects of the research and delved into general aspects like epidemiology, treatment and the links to obesity etc. This was followed by a a presentation from Dr Arkaitz Carrecedo brom beneficiart CIC BioGUNE on the latest advances in prostate cancer and metabolism.
After a short break it was straight into the first set of progress reports by the ESRs, their first opportunity to present a summary of their background reading, aims and preliminary results to the whole consortium and to face questions from supervisors and the other ESRs about them. This first set of updates continued the cancer theme, featuring the projects from ESRs based in Madrid, Bilbao, Munich and Covilha whe are working in this particular aspect of TRIB protein expression and regulation related to pancreatic cancer. It was a great opportunity to see how the different projects interlinked and provided some insights into the dierction some of them could take. To complement these updates and give some context, the supervisors from the same centers then each gave a short overview of their labs’ other interests.
To complete the day of updates the final session of the afternoon switched the focus to the role of TRIBs in adipose tissue with two presentations from the ESRs at Munich and Utrecht.
To close a very long day the ESRs spent some time together in a workshop session concentrating on the function and use of the ELN system that the consortium is using to share results, protocols and common reagents across all of the projects. It was a very useful practical demonstration of the advantages of using this type of tool where projects have several areas of overlap and can benefit from a co-ordinated approach. Meanwhile, the Supervisory Board held their second management meeting and finally, after 11 hours on the go, everyone joined up again to enjoy an excellent tapas meal and late night at Restaurant Albur.
Day 2, 8th October
The focus of the morning session on day 2 was genomics, starting with a very useful lecture from Dr Istvan Nagy from beneficiary SeqOmics on the basics of RNAseq and ChIP technologies. These are central to many of the ESR projects so there was a great deal of interest in the methodologies for preparing samples etc. Immediately following this we heard progress reports from the two ESRs who’s projects have a genomics approach: “The regulation of Trib 1 transcription” from Miriam Ruiz Cantos at QMUL and “miRNA-mediated regulation of Tribbles 1 and -3 expression” from Chiara Niespolo at Sheffield. To finish off the morning there was a shift to the bioinformatics aspects of transcriptomic datasets, with very useful case study illustration of methodologies by Dr Zoltan Hegedus from the Biological Research Centre, Hungarian Academy of Sciences then a presentation by Sumeet Deshmukh, who is the newest ESR recruit and who’s project will be focusing on the Bioinformatics approach for RNA-Seq differential differential expression data analysis. Finally, slotted in to the end of this session was a progress report from ESR Juan Salamanca, based at beneficiary Intelligent Pharma, who’s project is trying to model the protein-protein interaction between TRIB 3 and SIAH1.
In the afternoon, the final set of ESR progress reports was heard with five presentations from those focusing on the Immune Cell aspects of Trib proteins.
Time out for a group photograph on Day 2.
To finish off the day the subject switched to “Project Management in SMEs”, where the ESRs were placed in the hands of the two SME beneficiaries from the consortium. The first part of the session required everyone (ESRs and PIs) to work in small groups vying with each other to build the highest tower out of spaghetti and a few other random components. Great fun but a useful preface to the discussion on the need for “Agile Methodologies” in small companies and how these are essential to stay ahead of the game. This was followed by entertaining presentations on…….. and collaborating with the Pharma Industry, curiously titled “The Good, the Bad and the Ugly”.
Day 3 9th October
Time for the ESRs to relax a bit on Day 3, as the first part of the morning was given over to hearing from two external speakers: Alejo Efeyan from CNIO, Madrid on “The interplay between nutrients, metabolism and cancer”, and Maria Mittelbruun from Universidad Autonoma de Madrid on “Immune system metabolism in inflammatory diseases and ageing”. Both talks provided good context and background to the discussions that had been the subject of the previous two days. Following this a short session providing feedback on the ESR’s presentations from the first two days, in the context of style and delivery rather than scientific content, gave everyone time to reflect on how they might improve on their communication skills in future meetings. A very valuable exercise.
The second half of Day 3 continued the theme of “Communication”, with a very engaging special seminar on the essentials of academic writing by Iain Kennedy Patten. Iain’s clear and well reasoned message started with the need to really understand what we are doing and how we make our contribution to the scientific landscape so that we can identify the correct strategy for publication. He also demonstrated the structure of a good article and many of the pitfalls that can cause even the best scientific content fail to achieve the impact it might deserve because of the poor structure of the written paper. This was fascinating stuff, which was all the more powerful because it illustrated a written structure that was so simple when broken but little recognised when we actually do it . Everyone could not believe that four hours could pass so quickly.
ESRs discussing how they “Define their Contribution” during the Academic Writing Workshop
Day 4 10th October
And so to the final day, which started with another session in the communication theme, this time looking at how to run a successful journal club. The presentation, by Dr Claire Hutchinson from QMUL, demonstrated some of the key do’s and don’ts with some very relevant examples and tips from personal experience. The ESRs have been tasked with discussing journal articles in their bi-weekly videoconferences so they will be able to put the content of this session into practice very soon.
The final session of the week was a hands-on session of practical genome bioinformatics presented by Dr Zoltan Hegedus of the Biological Research center at The Hungarian Academy of Sciences. The ESRs went through the use of the Ensembl Genome Browser to annotate genes, compute multiple alignments, predict regulatory function and collect disease data. These techniques are useful to most of the projects under TRAIN.
So, after 3.5 days of intense work it was finally time to relax and the afternoon was spent in the sunshine exploring parts of Madrid or simply watching the world go by at a pavement bar. For those who had some stamina left though there was an opportunity to take in some culture at the Prado Museum, where Prof Guillermo Velasco and other members of the Madrid TRAIN group had laid on an interesting and informative tour of some of the most influential artworks, pointing out the scientific relevance of many of them. A great way to finish a great week.
Here are a few of the ESR’s impressions of the week:
Yodit (ESR 2, Nantes)
The first TRAIN_ITN workshop was in Sheffield, for most of us we have just started our PhD projects. We were apprehensive as we tried to register as much information possible and get involved in asking questions. After, via conference meetings twice a month and keeping in contact through social media platforms we have become close friends. Six months after our first meeting, we gathered again for the second TRAIN workshop session, this time in Madrid; welcomed by Prof. Guillermo Velasco and his team. We were all excited to see each other again and update each other on our lab work and our life in the new countries we have moved too.
We were no longer just observing our supervisors present, but we were presenting and chairing each other’s presentations too. We were all curious, asking questions, discussing among ourselves and giving feedbacks to each other. Rather than via email, I was now able to discuss experiment ideas, technical adjustment and protocols with the ESRs in person. Moreover, dig into the details of how I can collaborate with others. This discussion didn’t stop throughout breaks and meal sessions. I now had a greater understanding of immune-metabolism and Tribbles research. I left Madrid with full of experimental ideas, equipped with employing critical thinking in my experimental design and reviewing papers; and most of all I was motivated to get back to the lab and continue my work.
Jack (ESR 14, Madrid)
After having gotten to know each other a bit during the first meeting and through our bi-monthly online meetings, the second TRAIN workshop hit the ground running as we welcomed some new faces to the consortium. In this second meeting, we ESRs had the opportunity to spread our wings a bit and present our projects and related topics. For me at least, this made the meeting much more engaging and enjoyable.
The best talk, in my opinion, was that by Iain Kennedy Patten on Science Communication and Academic Writing. How he explained good writing, and bad writing, was quite enlightening. But the meeting didn’t just involve talks and presentations; the evenings spent socialising were also an important aspect. It was during dinner discussions that possible areas for collaboration between the students were helped solidified.
It was a shame really that the meeting had to end, as we had become a well-knit group of enthusiastic students, spurred on by the desire to do ourselves, each other, and our supervisors, proud.
Imogen (ESR 1 Utrecht)
Our second consortium meeting was held in Madrid, hosted by Prof. Guillermo Velasco and his group. During this time we presented our progress reports, discussed several common techniques and future works. In addition to this, we all attended many seminars from scientific writing to bioinformatics. We were also lucky enough to explore Madrid in the evenings thanks to several of our consortium members who know the city well. On the final day we all visited Museo del Prado with Prof. Guillermo Velasco and Jack Day as our tour guides. Overall it was a useful and engaging meeting, made even better by the warm weather and delicious food!
Paris (ESR 6, CIC BioGUNE)
Let´s start from the end. In the last day of our stay in Madrid, the sweet essence of art in Prado museum was a perfect complementary for our scientific minds, which have been experiencing an intense but fruitful 3-days long workshop at the University of Complutense de Madrid. While watching Saturn Devouring his son by Francisco Goya, I was digging down my mind and sorting all the things that I have learned in these days.
In spite of the intense time we spent at the seminar rooms, listening to the presentations one after the other and the stress we had for presenting our own work, I must point out how it helped us, students, to connect each other, to our own supervisors and to other group´s supervisors, not only in the seminar rooms, but also in the coffee breaks, at lunch or around the table of dinner in a sweet restaurant in the heart of Madrid.
During the workshop days, I had the chance to get to know every group´s initial work and results, experimental setups and future plans. Moreover, I learned a lot about how companies can be a one of the future options to be considered after I finished my PhD. We are in our first year of PhD but TRAIN has already started to train us to write our thesis in the perfect way by giving an interesting talk about the proper structure of a thesis or a scientific paper, which I found the most helpful one.
Last but not least, having the opportunity to meet all ESRs and supervisors not through the window of the computer – as we always have been meeting this way- but in real life was a great experience and we now feel ourselves more attached, which itself is a way to be more supportive for each other as we all are a family. Family of Tribbles !
Ziyanda (ESR 9 UBI) Our Madrid workshop was a worthwhile experience. This time round we all knew each other which made it more enjoyable. The 4-day event was filled with many interesting and useful aspects. From the thought-provoking presentations given by the students, supervisors and invited guests to the relaxed dinners and sight-seeing, every second of it was great! I’ve taken back so many ideas and ways to improve my project. The workshop helped build stronger bonds among us students and also with the PIs, which will be good for future collaborations. Now I´m excited and keen to work harder for the next one.