State of the lab 10 and 11 - the first years at ETH Zurich
Yet another lake by a mountain in SwitzerlandThis blog post is part of a(nearly) yearly series on running a research group in academia. This post summarizes years 10 and 11, the first 2 years after moving to ETH Zurich. It also marks the end of the first decade as a research group leader, which is meaningful only because we have ten fingers and use 10 as a base for counting but I digress. There has been a lot to adapt to in moving to a new country including all the basics of moving, re-building the group and starting teaching. It was a lot easier than the first time around since I didn ' t have to set up the group from zer...
Source: Evolution of Cellular Networks - November 13, 2023 Category: Cytology Tags: academia state of the lab Source Type: blogs
20 years of open science or how we haven't radically changed the way we do science online
Around 20 years ago I was a starting PhD student and it was an exciting time for the internet. It was the time of blogs, wikis and a large increase in public participation with more user generated content in what is commonly known as the start of Web 2.0. These were the times of web based online communities such as the now defunct Kuro5hin or the great survivor slashdot.org. I started this blog 19 years ago and I was also " hanging out " in an online community called Nodalpoint. Nodalpoint no longer exists but it was a discussion forum/wiki for bioinformatics with some of these discussions st...
Source: Evolution of Cellular Networks - November 16, 2022 Category: Cytology Tags: open science Source Type: blogs
Independent evaluation of AlphaFold-Multimer
AlphaFold2 has been widely reported as a fantastic leap forward in the prediction of protein structures from sequence, when sequence has enough homologs to build a reasonable multiple sequence alignment. When AlphaFold2 was released (Jumper et al. 2021) there were several independent reports of how it could also be used for the prediction of structures of protein complexes despite the fact that it was not trained to do so (Bryant et al., 2021;Ko and Lee, 2021;Mirdita et al. 2022). Together with the lab of Arne Elofsson, in work led byDavid Burke in our group and Patrick Bryant in Arne's group, we have shown that...
Source: Evolution of Cellular Networks - March 8, 2022 Category: Cytology Tags: original research Source Type: blogs
A closer look at the costs of EMBO publishing
There has been a lot of discussions on social media about the price that some publishers are coming up for publishing a paper in their journals - the so called article processing charges (APC). With some journals asking for values that are on the order of 10k and many scientists finding these values to be outrageous. Given that journals don't work to produce the research articles and get academics to do the evaluation, how can these journals claim the costs of publishing a paper to be anywhere close to 10k ? While I agree that these are outrageous values, I don't really believe that the price is mostly profit. A good sourc...
Source: Evolution of Cellular Networks - February 2, 2022 Category: Cytology Tags: publishing Source Type: blogs
State of the lab 9 - an informal report on the 9 years of EMBL-EBI
This blog post is part of ayearly series (or close to yearly) on running a research lab in academia. 2021 was the last of 9 years as a group leader at EMBL-EBI, which is the standard time given to group leaders to establish and run their labs at EMBL. For this year's blog post I thought it was a good time to look back at the full 9 years and I am going to (briefly) cover the time at EMBL with some numbers including giving an approximate account of the finances. This is something that I do with the group at the start of every year but it still feels strange to make financial numbers public. The scientistsA lot has happ...
Source: Evolution of Cellular Networks - January 19, 2022 Category: Cytology Tags: academia state of the lab Source Type: blogs
A not so bold proposal for the future of scientific publishing
Around 15 years ago I wrotea blog postabout how we could open up more of the scientific process. The particular emphasis that I had in mind was to increase the modularity of the process in order to make it easier to change parts of it without needing a revolution. The idea would be that manuscripts would be posted to preprint servers that could accumulate comments and be revised until they are considered suitable for accreditation as a peer review publication. At the time I also though we could even be more extreme and have all of the lab notebooks open to anyone which I no longer consider to be necessarily useful.Around 1...
Source: Evolution of Cellular Networks - June 10, 2021 Category: Cytology Tags: open science publishing Source Type: blogs
Lab move to ETH Zurich, the job search and fixed term PI positions
ETH Zurich (credit) Next January, after 9 years at the EMBL, I will be joining ETH Zurich as a tenured faculty of the Department of Biology with my research group hosted at the Institute for Molecular and Systems Biology (IMSB). I am really excited about this move and I think the IMSB is a perfect fit for the type of research that we do. We primarily use computational approaches to study the relation between genotype and phenotype with a specific focus on post-translational regulatory systems (more on theEBI website or myGScholar page). IMSB has a long tradition of method development in large scale measurements o...
Source: Evolution of Cellular Networks - May 21, 2021 Category: Cytology Tags: academia group Source Type: blogs
State of the lab 7 & 8 - The last years at EMBL
This is usually part of ayearly series of posts where I note down thoughts related to managing a research group in academia over the years. This post covers years 7 and 8 and it brings me now to the start of year 9, my last at EMBL. While I usually do one of these posts every year, with all of the craziness of 2020 I ended up skipping one. Year 7, group turnover 2019 was the year where the group fully turned over all lab members that were with us since the earlier years with 2 postdocs (Haruna Imamura and David Ochoa) and 3 PhD students (David Bradley, Claudia Hernandez-Armenta and Marta Strumillo) leaving. ...
Source: Evolution of Cellular Networks - January 29, 2021 Category: Cytology Tags: state of the lab Source Type: blogs
A year of SARS-CoV-2 research
This post may be premature but I feel like writing down some thoughts about the roller coaster that this year has been. At the start of the year, with the number of reported cases rising in Europe the EMBL and our institute (EMBL-EBI) decided to send everyone home as precautionary measure. As most of our group is computational, this has meant we have been working from home for most of this year. Early on, somewhat frustrated by not being able to help, I emailed a few people that could be working on the virus. Nevan Krogan replied saying our help would be useful and we joined the global effort to contribute to solving this ...
Source: Evolution of Cellular Networks - December 4, 2020 Category: Cytology Tags: academia Source Type: blogs
PlanS, the cost of publishing, diversity in publishing and unbundling of services
A few days ago I had another conversation about PlanS with someone involved in a non-profit scientific publisher. I am still sometimes surprised that these publishers have been very much reacting to the changes in the landscape. In hindsight I can understand that the flipping of the revenue model to author fees has been threatened for a long time but always seemed to be moving along slowly. Without going into PlanS at all, the issue for many of the smaller publishers is that they simply cannot survive under an author fee model because their revenue from the subscription would translate to an unacceptable cost per art...
Source: Evolution of Cellular Networks - May 30, 2019 Category: Cytology Tags: publishing Source Type: blogs
