CABANA – not just a shelter from the sun

You may have heard the name CABANA floating around the EMBL training programme, but you may not know exactly what it is. Here we present a handy guide to the project, its origins and where it stands now almost three years on from its launch.

PHOTO: CABANA logo
PHOTO: CABANA logo

CABANA is a capacity strengthening project for bioinformatics in Latin America. It aims to accelerate the implementation of data-driven biology in the region by creating a sustainable capacity-building programme focusing on three challenge areas – communicable disease, sustainable food production and protection of biodiversity.

Want to know more about the project? Check out this video from the CABANA consortium.

With just over a year left of the project, funded by the Global Challenges Research Fund (GCRF) – part of the UK Aid Budget, the capacity building element of the project is ramping up. A big part of the project is running a series of training events for the Latin American audience, something that began with the centralised events team within EMBL-EBI, but is now increasingly being operated in Latin America by the partners themselves.

CABANA has virtualised its training programme for the rest of 2020 and has committed to a fully virtual 2021 programme too. Check out the latest events on offer, or visit the new virtual training portal for the e-learning options.

Follow the CABANA project on Twitter or Facebook for the latest news and updates.

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Ada Lovelace Day 2020 – The women of computational biology today

Ada Lovelace. Source: Suw Charman-Anderson on Flickr
Ada Lovelace as depicted by Suw Charman-Anderson on Flickr

Ada Lovelace is often regarded as the first to recognise the full potential of computers and as one of the first computer programmers. 

In honour of Ada Lovelace Day 2020we are shining the spotlight on some of the remarkable women that we have met during our training courses this year. 

 


Who? Hema Bye-A-Jee
Job title: Senior Scientific Database Curator, EMBL-EBI
Where to find her? Hema is delivering the webinar ‘A Guide to UniProt for Students’ via the EMBL-EBI training website tomorrow (14 October 2020). It is full, but the recording will be available the next day.

PHOTO: Hema Bye-A-Jee
PHOTO: Hema Bye-A-Jee

Tell us a bit about your work, what are you researching currently? 
I am a scientific curator for the UniProt team and I primarily sift through scientific publications to annotate C.elegans proteins, but I get to find out about lots of proteins in many organisms. Engaging with scientific and non-scientific communities is a very important aspect of what we do. Not only does my role feed my scientific curiosity, but it also enables me to help others to look at their data in different ways; we prepare specialised workshops and webinars, such as the “guide to UniProt for students” which I shall be presenting tomorrow.

What does it mean to you to be a woman in STEM today?
It means a lot because I know that many struggles and injustices have been endured, and it is unsettling that battles are still ongoing in many respects. I believe that science is for everyone and earning a place at the discovery table shouldn’t be based on gender, age, race, or even who shouts the loudest. If you can see beyond what’s right in front of you and can question it, surely you should at least be deserved of an invitation to be in the same room as the table!

What are your aspirations for your career in the future? 
I am very fortunate because I get to read about something new every day. I hope to continue working at the forefront of scientific discovery and innovation and take forwards my skills in communicating complex scientific principles, and wish to help others achieve the most from their data in the intellectual property law field.


Who? Rea Antoniou-Kourounioti
Job title: Postdoc at the John Innes Centre
Where to find her? Rea was a recent speaker at the EMBL-EBI Mathematics of Life: Modelling Molecular Mechanisms virtual course. You can find her slides on our ftp site.

Rea Antoniou-Kourounioti
Rea Antoniou-Kourounioti

Tell us a bit about your work, what are you researching currently?
My work combines mathematical modelling and experimental biology to understand how temperature affects when plants decide to flower. I am currently part of the groups of Martin Howard and Caroline Dean, and our work focuses on the gene FLC, which is epigenetically silenced in response to cold. We recently discovered one of the temperature sensing mechanisms that affect this gene and compared plants adapted to different climates. We found that the levels of the gene in autumn are very important for their different responses, and we are now trying to understand the mechanism that determines these levels.

Who or what inspired you to enter a career in STEM? 
I was fortunate to grow surrounded by academia, because both my parents were at the University, my mother specialising in biology and my father in maths. Therefore, I had many role models, though the pattern of women in biology/men in maths was prevalent in my environment. However, I was very close to a woman mathematician (the first female professor of Mathematics in Greece) who would give me puzzles to solve at all the grown-up parties. Solving puzzles was my passion then, and so it remains, and there are so many unsolved puzzles in biology!

What do you hope the future of working in STEM looks like?
More focus needs to be put towards understanding the complex reasons that women leave science at all career stages such as a different perception of worth, both from the outside and the inside. Hiring and assessment procedures favour characteristics associated with men, e.g., I still remember the lack of confidence I have had to battle to make my voice heard in meetings. This is deeply rooted in the differently promoted values for boys and girls and needs to be battled there and in its consequences. Events such as the Nobel prize recognising women this year helps girls to see that science is (also) for women and gives them inspiring role models like I was lucky to have.


Who? Zuzana Jandova
Job title: Postdoc at Utrecht University
Where to find her? Zuzana is a speaker at the upcoming BioExcel Winter School on Biomolecular Simulations event. Applications are currently open.

PHOTO: Zuzanna Jandova
PHOTO: Zuzanna Jandova

Tell us about your work, what are you working on right now?
As a part of the HADDOCK team at the Utrecht University, I focus on dissemination and training of our software as well as my own research. In training, we prepare tutorials, organise workshops and summer/winter schools, answer questions on public forums and make software easier and more approachable to users. In my own research, I look at how the combination of a traditional docking approach with molecular dynamics simulations and machine learning can improve the prediction of protein-protein interactions. This is then applied in areas like antibody design, where we can engineer antibodies in pharmaceutical research.

What are your aspirations for your career in the future?
I would like to stay in the biomedical field, where I also started when I decided to study pharmacy. Working in research, more specifically academia gave me a lot such as critical thinking, data management and project planning which I would like to take further into a more applied area. Thus, working in a pharmaceutical company or research institute where I could focus on not only the first theoretical stages of drug development but also on the further use of the drugs and biologics on the market would be a good option for me.

What does it mean to you to be a woman in STEM today?
To be honest I have never thought about my gender as a key element for my career choice. However, I realise that women are still somewhat underrepresented in computer or technical sciences in general. This is also why I think it is important that we talk more about women in science which can be a great example and inspiration for younger generations. And the more recognition we get, the more it becomes a norm to take women as an equal, respectable and knowledgeable part of the society. 


Name: Alessandra Villa
Job title: Senior Researcher at KTH Royal Institute of Technology
Where to find her? Alessandra is a speaker at the upcoming BioExcel Winter School on Biomolecular Simulations event. Applications are currently open.

PHOTO: Alessandra Villa
PHOTO: Alessandra Villa

Tell us about your work, what are you working on right now?
I was educated as a chemist. Early in my career, I realised that I was very interested in solving biophysical problems, thus I decided to do it using molecular modelling and computer simulation. My work focuses on improving molecular models to better describe how macromolecules interact. This can deepen our understanding of their function. Higher-education teaching has also played a key role in my career. Currently, I am working at the European Center of Excellence BioExcel, applying my expertise to promote and improve the use of advanced scientific tools.

What are your aspirations for your career in the future?
My aspiration is to contribute to building a lively environment that combines high-level teaching and research and to move to a coordination role with more decision power.  

What does it mean to you to be a woman in STEM today?
To be a scientist in STEM means to be able to understand, to contribute, to deepen our knowledge and to teach/disseminate on how nature (in my case molecules) function. In addition, it also means to be able to critically evaluate any new information and to be curious about things in general.  To be a woman in STEM is to be a scientist in STEM.

In the later stage of my career, I have realised that as a woman in STEM I always had to really demonstrate what I know. I was evaluated for what I did and not for what I could do, and further steps in my career may be full of “unpredictable” obstacles.


Name: Molly Gasperini
Job title: PhD Scientist, Octant
Where to find her? Molly was a speaker at a recent EMBL-EBI Industry Programme virtual workshop: High Throughput of Assessment of Functional Human Mutations. EMBL-EBI Industry programme members can download the slides from the members area.

PHOTO: Molly Gasperini
PHOTO: Molly Gasperini

Tell us a bit about your work, what are you researching currently?
I am developing high throughput functional assays to screen drugs against neuropsychiatric receptors at a scale and speed never before achieved. Find out more.

What does it mean to you to be a woman in STEM today?
I am extremely fortunate to be a part of science at a time where women generations before me (like Ada) have broken down many previous gender-based barriers. Though improvement is still required, most parts of science are largely welcoming for female scientists. Now, it is our responsibility to break down existing barriers for scientists who don’t identify with the racial, sexual-identity, or economic majority of the scientific community.

What are your aspirations for your career in the future?
I have always struggled with whether to climb the traditional ladder of leadership, though such job advancement takes you further from the bench and Rstudio, and into more meetings! Fundamentally, I hope to always continue working on thrilling tech dev as part of a rigorous and fun team.


Follow #ALD20 on Twitter to celebrate even more women, advocates and educators in STEM.


Authors

PHOTO: Michelle Mendonca
PHOTO: Michelle Mendonca

PHOTO: Rebecca Nicholl
PHOTO: Rebecca Nicholl

PHOTO: Emily Pomeroy
PHOTO: Emily Pomeroy
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5 Years Quantitative Proteomics Course

 

Meet Christina Ludwig (CL), Jeroen Krijgsveld (JK) and Mikhail Savitski (MS) – organisers of the EMBO Practical Course: Quantitative Proteomics: Strategies and Tools to Probe Biology (21 – 26 June 2020). This year marks the course’s 5th anniversary and since 2016 it has grown in popularity and application numbers, reaching 164 applications for 24 seats in 2018. Christina, Jeroen and Mikhail share with us how the course has developed over the years and what their vision is for its future.

 1.  This year marks the 5th anniversary of the Quantitative Proteomics course. Back in 2016, why did you decide to organise it?

JK: The main motivation to initiate the course was because proteomics has become a mature technology that is increasingly being used by biologists to identify proteins, their modifications, interactions etc. However, few biologists have direct access to mass spectrometers, so they use them via collaborators or core facilities. They then get the results in a tabular form, often in a large excel sheet, from which they extract biological interpretation of the experiment. Importantly, we felt that the area between handing in a sample for mass spectrometric analysis and receiving the results was largely a black box. So in the course we aimed to demystify this, and explain the principles and strategies to generate information from raw MS data, and to train them in the use of computational tools to achieve this. Also, we aimed to give insight that proteomics can be done in various ways, so that participants may design their experiments such that they best address the question they are looking to answer. Finally, we aimed to equip participants with some terminology that will help them to communicate with their MS-collaborators, and ask the right questions. Because in many cases proteomics remains a team effort!

2. How has the course developed since?

JK: Proteomics is a very broad field with many mass spectrometric approaches, methods for data analysis and biological applications, making it impossible to cover this in a 1-week course. While in all editions of the course we have maintained a core that explains the main principles in proteomics and covers all of the current state-of-the-art quantitative technologies used in proteomics. Additionally, we have included other elements that varied over the years, to highlight emerging topics or specific application areas, e.g. in structural biology or immunology. This year, we are happy to include a module focusing on statistical analysis of large-scale proteomic data, which is a recurrent issue in almost any proteomics experiment.

3. How do you choose which bioinformatics tools to cover in the course?

JK: There is an increasing number of bioinformatic tools that can analyse the same data using different underlying algorithms. Several of them have matured a lot over the years, making them more robust or have additional functionality. It is not always easy for anyone to know, when looking for an ‘analysis pipeline’, which tool can be best used. It can actually be a bit confusing that the same data can produce different results depending on the tool that is used, while at the same time none will be wrong. So instead of telling which tool is the best, we explain some of the underlying assumptions and the influence one has by choosing certain settings. I think for a researcher it is more important to justify how the data were processed, instead of saying that they used a certain software tool.

4. What could the techniques in this course be used for in the bigger picture?

CL: Proteomics technologies have reached a level of comprehensiveness, throughput and quantitative quality that was inconceivable just a few years back. However, applying proteomics to biological projects still requires lots of knowledge about experimental design, optimal sample preparation, most suitable mass spectrometric technologies and statistical interpretation. If we manage to bring both worlds together and teach biologists about the power, as well as the caveats, of proteomics, I think this will really impact life science in many aspects and truly transform the way how scientific projects are carried out for many scientists all over the world.

JK: I agree. Demonstrating the versatility, and thereby the potential and broad utility of proteomics in different contexts is sometimes an eye-opener for course participants. Actually, it is interesting and useful that participants come from all corners of biology, from paleobiology to clinical biomarker discovery. Having those together in a room for a week and interact, with proteomics as the common interest, is fascinating to see as an organiser. And we explicitly facilitate such interactions in discussion groups – it is an important goal of the course.

5. How do you see this course growing in the future?

CL: I think one special feature of this course, compared to other proteomics courses, is that its rather familial in character due to the small number of 24 participants, and that they come from purposefully different countries and research institutes. This rather small group size is optimal in terms of group dynamics and allows lots of personal exchange between participants and speakers, as well as an optimal support during the practical sessions. Therefore, I hope also in the future the small and familiar atmosphere of this course will remain.

JK: What I also hope, and what we’ll try to achieve, is to remain up-to-date and include novel technologies that are emerging. After 20 years of steep development in mass spectrometry, one would expect that this levels off at some point, but this is not the case at all – it is actually difficult to keep up with what is happening, and with what is possible today that you would not dare to think about yesterday. Therefore, a remaining goal for us is to invite speakers and trainers who work at the forefront of technology, but who can also bridge this to important biological applications. This is what excites us as organisers, and we hope that this will help to make this one of the courses to go to for younger generations of scientists, and get infected too.

6. What motivates you most about your work?

CL: What I really love about heading a proteomics core facility is the huge variety of cool scientific projects you get exposed to, as well as the fact that you work closely with lots of very different scientists coming from completely different scientific disciplines. Every project and every collaboration partner challenges you in terms of diving into a new research area, providing an optimal proteomic workflow and also teaching and educating your collaboration partners in understanding their proteomic data.

MS: The fact that you have the constant possibility to come up and implement creative ideas is incredibly rewarding. Also the fact in research you are constantly generating results that are the first of their kind. There is always an experiment done that has not been done by anyone before and you are the first to see the results. I also love the academic environment the freedom and craziness of it all.

7. Why did you end up in the field of Proteins and Proteomics?

CL: Already during my Chemistry studies all the “biochemistry” lectures and practicals that focused on proteins and life sciences were by far the most interesting subjects for me. During my PhD, which I did in the field of protein engineering at the TU Dortmund, I studied a specific class of proteins, so called inteins, but I hardly applied any mass spectrometry during that time. However, for one specific experiment I used for the first time MALDI-MS to identify the reaction products of a set of purified inteins. My MALDI measurements showed the occurrences of an unexplainable loss of 18 m/z for one of my inteins. First I thought I did a mistake and was very frustrated. But when I repeated and further investigated my samples using also ESI tandem mass spectrometry I could proof the existence of a very interesting cyclic protein-intermediate, which actually helped me explaining the underlying protein splicing mechanism. This turned out being the most interesting result of my whole PhD.

MS: I originally was very focused on pure mathematics. By chance I had an encounter with Roman Zubarev who was a new professor at Uppsala University at the time. His drive, energy and passion for science convinced me to switch fields from mathematics to mass spectrometry and proteomics, which I never regretted.

8. What could you not do without in your life?

CL: Well, as a mother of two beautiful kids the very first thing I could not do without in my life is of course my family :)! And together with my family we love being outdoors, ideally in the Alps, either on (mountain)bikes, rock climbing or hiking. Living without mountains and outdoor activities would be very hard.

MS: First and foremost, my family! Second is physical activity. I love science and I love working a lot, but it takes its toll physically and mentally. My perfect way of recovering and getting the energy back is ideally by rock climbing, running and being out in nature in general.

9. If you would get the chance to meet a famous person – no matter if this person is still alive or not – who would that be?

CL: As a hobby climber I would really like to once meet Alex Honold, who is a world famous free-solo climber who climbed many of the most difficult and exposed climbs in Yosemite National Park without rope. Alex seems in interviews and videos like a really nice and funny guy, but I believe his brain must function very differently than mine when it comes to fear of height, so I would love chat with him about that ;).

MS: I was always interested in mathematics as well as computer science. It would have been fascinating to meet Alan Turing and discuss his vision of how things would develop based on what he knew back then. Incidentally, he was also a really excellent long distance runner with sub 3 hours’ marathon times. It would have been exciting to have a discussion over a run on the countryside :).

10. Which was the best decision in your career so far?

CL: I think the best decision for my career was to perform my Postdoc in the group of Professor Ruedi Abersold at the ETH Zürich, because this has really been the door opener for my career so far. When I finished my PhD it was actually not easy for me to decide for a postdoc in the field of mass spectrometry, because I hardly had any MS experience (I only performed this one MS experiment that I already described above ;)). And starting in a proteomics expert lab as a postdoc who had never really done proteomics before was definitely not easy in the beginning. But I did learn a lot of new things fast and ultimately this allowed me to bring together the two different expertises from my PhD and my Postdoc, which I do believe is a big advantage for any scientific career.

MS: Professionally, I think doing PhD in mass spectrometry was probably the best decision I have made so far. That early in your career, one still knows very little of the world and some luck is definitely required.


Interested in this course? Apply by 22 March!

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Meet the Trainer – Paolo Ronchi

PHOTO: Paolo Ronchi

Meet Dr. Paolo Ronchi, scientist in the Electron Microscopy Core Facility (EMCF) at EMBL, which helps users answer their biological questions by developing strategies and workflows.

Paolo first joined EMBL in 2008 as a PostDoc to study  the biogenesis of the Golgi apparatus after removal of this organelle from living cells by laser nanosurgery. 

Why did you choose to become a scientist?

During my studies, I was always more interested in literature and philosophy. However, when I had to decide for a university subject, out of curiosity I opted for something different: a new biotechnology course had just been opened and I enrolled. Despite this accidental start, I now think that a scientific career has been a good fit for my critical and curious mind.

Where do you see this field heading in the future?

It is very difficult to foresee where the developments are going to bring us. A few years ago, due to the developments in fluorescence proteins and light microscopy techniques, probably not many people would have bet on a bright future for electron microscopy (EM). Now the field is more active than ever, with 3D EM and correlative light and electron microscopy being key to new discoveries in biology. In the near future, I am convinced that the goal of the EM community should be to advance our methods (from sample prep to image analysis) to a higher throughput, to finally make EM a quantitative tool.

How has training influenced your career?

Working in a facility and being highly involved in training, I  experience daily how important courses are to disseminate knowledge and network with a community of experts. Furthermore my personal experience shows how attending a course can change your career, even many years afterwards. At some point during my PhD studies I realised I needed to perform some EM experiments. Therefore, I applied to the course on “Electron microscopy and stereology in cell biology”. It was a great experience, I learned a lot and, when I went back home, I could finally carry out the experiment that was missing for my thesis. In addition to this, I got to know many electron microscopists, including Yannick Schwab, who was a student of the course that year. I do not know whether the good memories of  that time played a role in getting me a job when, 10 years later, I applied for a position in the EMCF at EMBL (which Yannick is now heading),  but for sure it helped my confidence to start a new job.

What is your number one tip for people looking for scientific training?

Even though nowadays you can find all kind of tutorials online, I believe that attending a course in person is still key because of the networking possibilities that it gives. Getting the best experts to sit with you and think about your questions and problems is incredibly valuable. And when you go back home, you will remain part of a community that is in touch to share experience and tips.

If you weren’t a scientist, what would you be?

A professional cyclist  🙂

You are organising the EMBO Practical Course “Advanced Electron Microscopy for Cell Biology” (16 – 26 June 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

I think this course is really unique in many aspects. First of all, hands-on practicals are not just demos by the experts, but the students also have the possibility to learn using their own samples. In addition, the almost 1:1 ratio between students and trainers gives everybody the chance to be trained individually at the level they need. It is not by chance that many leading electron microscopists of today have attended this course in the past.

Interested in this course? Apply by 24 March 2020.

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Meet the Trainer – María del Mar Vivanco

PHOTO: María del Mar Vivanco

Meet María del Mar Vivanco, Team Leader at CIC bioGUNE in Bilbao, Spain. Maria is one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020).

What is your research focus?

I am interested in cancer heterogeneity, why some cells respond to therapy while others do not, thus contributing to development of resistance and metastasis. In particular, I am intrigued about the complex effects of transcription factors, which are required for normal physiology of the mammary gland and are also implicated in tumorigenesis and development of resistance to therapy in breast cancer.

Why did you choose to become a scientist?

When I was young I had a variety of interests – psychology, physics, art, biology… However, I was intrigued by science and anything related to DNA and its regulation. Then I did my PhD at EMBL Heidelberg (Gene Expression Programme) and discovered the opportunities in research for identifying problems, looking for solutions and the thrill of finding some of the answers…and I was hooked!

Where do you see this field heading in the future?

Despite significant progress in cancer research and clinical advances, breast cancer still is the most commonly diagnosed cancer – one in eight women will develop this disease during their lifetime – and it claims the lives of more women than any other cancer, plus men can also get breast cancer. This highlights the unmet clinical need for improved strategies for prevention, early detection and more efficient and specific treatments in order to accelerate progress and help more patients survive the disease.

One of the features that characterises breast cancer is its heterogeneity, both among patients and within each patient tumor. This heterogeneity is found at molecular, phenotypic and functional levels, complicating diagnosis and challenging approaches to therapy. Currently, huge efforts are dedicated to understanding this heterogeneity at all levels, including at single-cell resolution, which is anticipated to open new possibilities for more efficient and specific anti-cancer therapies.

How has training influenced your career? 

Doing my PhD at EMBL marked the way I envision science, and this vision was reinforced and developed further at UCSF. Science can – and SHOULD – be fun. Later on, funding struggles and the current publishing madness have somehow taken a toll on the fun element, so I just have to remind myself sometimes that science is still exciting!

If you weren’t a scientist, what would you be?

An artist.

You are one of the organisers of the EMBO Practical Course: Techniques for Mammary Gland Research (1 – 6 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

Some of the techniques practiced at this course are specific for the mammary gland and thus it provides a solid base for researchers starting in this field. In addition, there is a significant emphasis on imaging and comparison of mouse and human studies, the two major systems for looking at normal physiology and cancer research that, when combined, offer great insights into this heterogeneous disease. In addition, having the opportunity to work alongside other trainees contributes to the establishment of a network that may be helpful in the future. Cancer is a very complex problem, and having collaborators with different views and expertise will be very useful in your career.

Interested in this course? Submit your application by 8 December!

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