After we ESRs had participated in the 13th International MaxQuant Summer School on Computational Mass Spectrometry-based Proteomics, the opening dinner of the consortium meeting was the first time that all PROTrEIN members, incl. supervisors, actually met in person. The venue was amazingly beautiful and close to the sea. Where we all enjoyed a delicious dinner, with the added bonus of a beautiful night time sea view.

ESRs and supervisors attended the consortium meeting on September 12 and 13. The meeting featured presentations of the various work packages, keynote addresses, reports, and a meeting of the supervisory board. The «Management and Coordination» presentation by the PROTrEIN coordination team opened the work package presentations. An overview of previous sessions, including «scientific project planning,» midterm check, and summer school, was given at the beginning of this presentation. It went on to talk about internal reporting before citing the impending deadlines. Lastly, a little overview of Ghent Winter school. The nicest part of the meeting was the speed dating session when all ESRs had been given a chance to briefly introduce themselves to other project supervisors.
The ESRs were well-prepared the following day to provide an update on the status of their research work. Many of us ESRs were rather anxious, not only because of the supervisors, but also because of the «time machine» that was set up to inform us of the allocated time. Nevertheless, everything went smoothly, and we received many useful ideas from the other supervisors to enhance our direction.

«Novel machine learning predictors» was the first work package presented by five of the ESRs. The next six ESRs presented their works about «New algorithms for mass spectrometry raw data processing». This series of presentations was completed in the afternoon with «Integration and visualization of omics data» presented by the final four ESRs.

After a long day, Jonas had planned a surprise cooking workshop for us. It was a great team-building experience where we made tasty and colorful tapas. We were instructed by two very nice chefs, they divided us into two groups of warm and cold tapas, and of course, they didn’t forget the vegetarian options. The chefs first provided us with instructions and recipes, which we then heartily enjoyed. Our favorite tapas were the salmon and avocado tartar with pistachios mayo, and cod fritters with honey allioli. Even thinking about those fantastic tapas right now makes us want to go back and try everything over and over again.

The second day of the consortium meeting started with keynote lecturer Juan Antonio’s presentation on open-research and data reusability. The day was followed by presenting the remaining three work packages and discussing the upcoming winter school. The consortium meeting ended with supervisory board and coordination meetings, and all ESRs went to ELISAVA to start their science communication course.

Science Communication workshop

Design thinking for scientists was the first module of the workshop on science communication, and when we were asked at the beginning of the course “What we are expecting from this course?”, most of us thought it would be some spoken practice for our project presentations and visuals. However, it turned out to be much more than that.

Blanca Guasch steps in to explain how to apply design techniques to make our research more fruitful and efficient.  Design thinking involves several steps, including Empathize, Define, Ideate, Prototype, Test, and Implement. We created individual collages to illustrate the design thinking module Empathize, describing ourselves imaginatively with the aid of printed images, and describing how we are contributing to the PROTrEIN project.

Another interesting exercise that we ESRs had done is to put our names on the PROTrEIN WPn map according to the importance and relation of our contributions to each module of the design thinking process. Then, for the Ideate section, we discover the links between various ESRs and how they relate to one another in terms of project goals, secondments, and research methodology.

With the help of different metaphors, ESRs described the work bundles and processes like explaining machine learning, cross-linking concepts, etc.  After expressing our analogies to the group, we took into consideration their responses. After this engaging session 1, we all had some constructive ideas to use in our daily lives.

On the second day of the course on science communication, Blanca began the session with «Presentation designs for scientists,» another fascinating and crucial module for ESRs. This lesson focused on speaking well, taking the initiative, and being creative in our presentations. To keep things simple, avoid presenting too much information at once, emphasize the importance of consistency and typography, employ various styles according to the situation, and utilize a variety of formats and resources. 

Ane Guerra started a fascinating discussion on science communication storytelling and explaining stories. We completed some exercises as part of the story-telling process by describing the major difficulty we encountered when describing our project and the qualities that stand us apart from the others. Also, most of us ESRs defined our project as if we were a superhero, along with its foes, strengths, and nemesis. Being able to connect your project with some superpower heroes was, in my opinion, not an easy task, but most ESRs were able to accomplish it creatively. Then, we got some tips for developing story-telling skills in our research, including the use of a clear message, consideration of the audience, and the communication context. 

In the explaining stories session, we discovered that we should be aware of the audience when discussing our research and should stick to the core idea the entire time. 

“The best storytellers deliberately listen, watch, and read.” 

The session concludes with some helpful advice on how to improve our public speaking abilities, including knowing your audience, taking breaks, dressing appropriately, using our hands/voices effectively, and soliciting feedback.

Another relevant and interesting session for us ESRs is data visualization which is to embrace scientific complexity and transform it into a sympathetic visual story that improves all of its best features. 

We then discussed the process of mapping facts to visual structures, known as visual encoding. After that we went through how people in ancient times shared information about data I-e, the 1945 Molecular model of penicillin by Dorothy, and also discussed some good books which are based on data and visualizations.

In the last section of the course, we ESRs demonstrated our creativity by writing a video script while taking the public and expert audiences into consideration. A script for each audience had to be written according to a set of rules and to last for 60 seconds. Furthermore, we ESRs had been given the opportunity to present our posters and received feedback and discussion from our fellows and mentors. 

Last but not least, Jonas Krebs, all the mentors and the funding body deserves praise for organising such a relevant and informative science communication course for us ESRs. From this course, we have learned that better communication abilities enable researchers to share their discoveries with a wider audience and strengthen links within their scientific groups.

The post Recalling memories of our first in-person project meeting and SciComm training school in the beautiful city of colours ‘Barcelona’ appeared first on PROTrEIN.

But the general public cares less about research papers and is more interested in blog posts such as «Is your cow cheating on you?».

But then, there is a that one moment when you have to win a bet against your friend who thinks that «Cows can hear infrasonic sounds» and you need to open Wikipedia (*coughs* Microsoft Bing) to settle it. Or that time you had to write an assignment on «Cow hybrids”. Yep. One of the authors of this blog is obsessed with cows.

Anyways, Wikipedia to this day remains an important repository of high quality articles on almost any topic you can think of. To this end, we participated in a Wikipedia Hackathon that would facilitate addition of proteomics articles to the growing Wiki database.

So what is that we did on Wikipedia?

All PROTrEIN network early stage researchers participated in the wikipedia hackathon. We didn’t just learn about articles, but also approaches to publishing open access data to Wiki data.

Along with the mentor, Toni Hermoso, we created a web page in wikimedia entitled PROTrEIN Editathon (https://meta.wikimedia.org/wiki/PROTrEIN_Editathon_2022) we learned mainly how to edit into a wikipedia page starting from creating paragraph and subparagraphs into adding images into wiki images and then use it for our articles, we created multiple proposals for related terms and articles to the field of proteomics and mass spectrometry.

One article that we wanted to feature as an example is a Maxquant one. So as you see in the following figure, We created a wikimedia image for the software Maxquant, where we added the article for defining Maxquant alongside a figure for the software logo and viewer interface, we also added links and dates.

We learned how to create links, it works similar to hyperlink on the Microsoft Word processor. Alongside to citing, with automatic citation an editor can simply copy-paste the URL, and it will generate a citation. Whereas, manual citation requires the editor to enter the details of a book, journal, article, or website. After making edits, it is time to leave an edit summary about the changes that have been made to the wiki page.

This Wiki Hackathon took place within the framework of Computational Proteomics MaxQuant Summer School 2022 on September 5-6, 2022.

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The whole process of organising the summer school can be summarised in four different steps:
1) finding the venue to host the event
2) advertising the event
3) registration and booking
4) setting up the event

Finding the venue to host the event

In January this year, I joined the summer school organisation committee, which was composed of my supervisor Jürgen Cox, one post-doc and another more experienced PhD student that has already organised summer schools in previous years. When we discussed possible locations of the event, it was immediately decided to go to Barcelona, not only because of the sun, but also due to the logistic easiness (the MQSS took place there already once in 2018). Besides, Jürgen’s lab has contacts there (Eduard and Jonas from CRG) that were of great help. The initial phase consisted mostly of meetings with people from the agency that helped us with the organisation (Crea Congresos) and to decide when and where to have it. Once a venue that fulfilled the main requisites was found the real organisation from our side started and I got more involved. Such main criteria for the decision were: enough space for 200 participants and their posters, audio and video appliances and technical support and lastly being easy to reach. In this part most of the work, like visiting different venues and being sure of which services were ensured, was done by our counterpart in Barcelona. We were lucky that with their help we could convince the «Centre de Cultura Contemporània de Barcelona» (CCCB) to host the event one more time, same as in 20218.

Advertising the event

The first step was to design a nice logo and then set up the webpage. These were my initial tasks. I took this opportunity also to practice my skills in html and Adobe Illustrator. In particular, designing the new logo was something I enjoyed a lot, since I have always drawn and liked art. In other words, it was a great way to apply art to science.

Once the drafts were approved and the website was set up, it was time to start advertising the summer school through social media (e.g. Cox lab’s and Max Planck’s twitter account) and through sending emails to all previous years’ participants. In the meanwhile, the five main speakers were found and a first conference program drafted, both done in collaborative efforts. Lastly, Crea Congresos prepared the registration form and opened the bank account where to receive the conference fees from participants.

Registration and booking

As soon as we had set the registration deadline on mid May, the priority went to prepare the budget. All expenses were calculated by Crea Congresos, we checked them and added a buffer for eventual last moment expenses (an issue that indeed happened). On top of that, taxes were added and then 170 was set as the minimum required number of participants in order to cover all expenses. The registration fee for each person was calculated accordingly and the registration form opened. Assisting with the budget report was something totally new to me, but also helpful to get an idea of the costs that such event produces. Honestly, I have never dealt before with such an amount of money in my life. From this point on, we spend most of the time with taking care of public relations, since there was an average number of 8-10 emails per day from people asking for more information. The date to close the registration was at the end postponed to August. After that, we could proceed with booking the restaurant and social activities. Once we reached the second half of August, all participants that registered were contacted again in order to know if they wanted to present a poster and which social activity they wanted to join.

The week before the event, the spreadsheets with all this information were sent to Crea Congresos to let them know about the exact numbers. We organised all necessary documents and data (like MaxQuant, Perseus, tutorials and practical exercises) and transferred them to individual USB pen drives that we planned to give to each participant. Lastly, a new Zoom subscription was purchased in order to allow an online participation of the summer school and a new registration form for online participants was opened.

Setting up the event

Just few days before the start of the summer school, it was time to move to Barcelona to set up the venue and test appliances to be sure everything was ready for Monday. From that moment on, luck was not very much on our side. One small issue was that there has been some delays in the preparation of the USB sticks that we planned to give to attendants, but that was solved easily through all collaborative efforts during the weekend before. The bigger issue was a strike that caused flights to Barcelona to be cancelled, all except mine. This has been quite a big deal since on the Friday before the start we were supposed to visit the venue and test all the equipment. At the end we managed to solve everything thanks to the help of the people from Barcelona and the technicians, and all was set and ready for the event to start. The flight issue was exactly one thing we were worried about, especially because it was something we could not do much about it. At the end, it was a good reminder of Murphy’s law: “anything that could go wrong will go wrong”. Lastly during the weekend also the rest of the lab managed to arrive and we all prepared the material and rehearse our talks.

Finally it was time for the summer school to begin and about this I will not write much more since everyone from the PROTrEIN-ITN was there. The final program can be found on the MQSS webpage.

Honestly, there has been also a particular moment during which I cursed being one of the organizers and it was during the joint dinner on Wednesday. That day we kept an easy schedule for participants: social activities like tours or sport in the afternoon and then a dinner all together in a nice restaurant close to the sea. Unfortunately, my talk was exactly the next morning and there were some more data needed by participants that we could not give through the usb sticks. This meant that during the free afternoon I had to prepare my talk and then had to leave the dinner earlier in order to prepare the email that was sent to all participants with the aforementioned data. In other words I missed a nice evening and partying while some of my colleagues did not. Have a look at the picture above to get what I mean, for the record I was writing emails at that moment. Well, at least I did not have a hangover the day after.

In summary, it has been a nice experience, even though doing everything took a lot of time and there has been some stressful moments in particular during the last days. It was also a good opportunity to meet other researchers working in proteomics and to get a feedback from them regarding our general work. Lastly, when the event was over, it was also a great satisfaction to have been part of the organisation and seeing that participants appreciated it and had a good time during the week.

The post Organising a large event as a first year PhD student – behind the scenes of the MaxQuant Summer School 2022 appeared first on PROTrEIN.

After having everyone connected in the Zoom session, Jonas Krebs and Eduard Sabidó launched the day with some introductory slides on the project’s organization, funding and timelines. It was an ideal recap of things that we had already looked up in the previous months (we were impatient, ok?), but also some helpful new information was thrown in, such as a proposed schedule for regular ESR meetings etc. The rest of the day was filled with activities to break the ice between all members and get them to interact in a fun setting. It can be difficult to achieve these goals in a videoconference setting, but we should congratulate all the people that were involved in organizing the event, such as Anna, Imma and Damjana from the CRG Training Unit. They had done an amazing job, not only with all the events and activities that were planned (and that we will go over below), but also for the simpler details such as the music playing in Zoom during the coffee breaks.

A world-wide connection

One of the first ice-breakers we did, was to open up a virtual world map and place a pin on our current location. From Tamper, Finland to Mangalore, India and from Jeonju, South Korea to Rockville, USA, there were pins scattered all around. It is an impressive feat of scientific project such as PROTrEIN, to create such diverse networks of individuals across all these time zones. And soon enough, we would all be on the European continent doing exciting research!

Express your feelings

A couple of weeks before the event, we had been asked to find and post a GIF image each to describe their feelings about ourrespective PhD projects. The old proverb says “one picture is worth a thousand words”, so you would think that an animated one would be adequate to describe these feelings. Well, wrong! There were so many feelings and thoughts in our minds regarding our forthcoming PhD project, and some of them do not even have a word dictionary. Nonetheless, we all tried our best to focus on one of those feelings and we ended up with a highly expressive wall of GIF images.

Speed-dating

Writing this post several weeks after the events, we still vividly remember the reaction of Eduard at the end of this particular section: “Wow! This was… intense!”. It was the most suitable reaction to what was otherwise an incredibly fun activity. Thanks to Zoom’s functionality, pairs were formed and placed in separate breakout rooms with precisely two minutes to quickly get to know each other, before being abruptly interrupted and thrown into another breakout room with someone new. Do you remember the beginning of this post where we described how can a few seconds feel so long when you open an important email? Well, these 2 minutes in a breakout room with someone you barely know felt like the complete opposite! It provided mixed feelings of excitement to discover who your new partner was, while at the same time carrying over the frustration from being interrupted mid-sentence with the previous. Now we look forward to the next event (1^st Winter School in Zurich) and hope that we are able to meet in person and complete all these unfinished conversations.

Advanced Proteomics course

After getting familiar with all ESRs and supervisors, it was time to focus on the concept of proteomics. We took the online advanced proteomics course from the 13th to the 17th of September, and each day consisted of two main parts. In the first part (morning), a series of lectures were provided by our supervisors and other invited professors. These lectures were provided in-depth information on various topics such as data-dependent and –independent acquisition, manual spectra annotation and even reconstruction of ancient protein sequences. We gained a lot of insight into some core, but also advanced, concepts of proteomics. One of the most interesting sessions was about the applications of machine learning to proteomics data. In the next part (afternoon), we experienced some hands-on workshops where ESRs were separated into groups to work together on a particular problem. This experience was really challenging and also exciting, mainly because we had to network with other ESRs, coming from different backgrounds, to resolve an issue at a specific time.  

Open & Responsible research

The last three days of the Summer School were dedicated to the topic of open and responsible research. The topic itself is broad enough, and through some excellent seminars/workshops we had the chance approach the matter from a variety of angles. Going into details would make what is an already pretty long post interminable, but we had the chance to learn about concepts such as data openness (and particularly the FAIR principles), result reproducibility and the various options and procedures that go into authoring and publishing scientific articles. Best of all was the opportunity we had to openly question and discuss these important matters among ourselves.We hope these are topics that we will have the chance to revisit in future posts of this blog!

We hope these are topics that will be revisited in future posts of this blog!

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