diff --git a/_posts/blog/2020-01-23-2020-01-23-lab-meeting.md b/_posts/blog/2020-01-23-2020-01-23-lab-meeting.md new file mode 100644 index 00000000..ce9e1632 --- /dev/null +++ b/_posts/blog/2020-01-23-2020-01-23-lab-meeting.md @@ -0,0 +1,173 @@ +--- +layout: post +title: Lab Meeting on 23 January 2020 ### REPLACE `DATE` with the date, eg: 18 July 2019 +categories: blog +excerpt: Notes from the group's weekly lab meeting ### ADD a short description (or keep that one if you'd) +tags: [lab-meeting] ### INSERT TAGS IF APPLICABLE +image: + feature: +link: +date: 2020-01-23 ### UPDATE date +modified: +share: true +author: kirstie_whitaker ### CHANGE to your author name (in _data/authors.yml) +--- + +Today was an open agenda meeting so we got to dig into everyone's updates in a little more detail than usual. +Keep reading for the fantastic discussions on leadership and mentorship, applying for a job, chairing sessions, and building community. + +Happy new year to everyone celebrating the lunar new year πŸ€ πŸŽ† πŸŽ‡ + +## Celebrations and cool things to share + +**Kirstie** gave a talk at [OpenMR Benelux](https://openmrbenelux.github.io/) on Tuesday (slides available at doi: [10.5281/zenodo.3615258](https://doi.org/10.5281/zenodo.3615258)). +She had a really fun day accompanied by lots of FOMO for missing the hacking days on Wednesday and Thursday. +Her particular huge highlight was meeting [Agah Karakuzu](https://twitter.com/agahkarakuzu) and [Christina Bergmann](https://twitter.com/chbergma) - two people she's collaborated extensively with but whom she'd never met in real life! + +Kirstie is also keeping her fingers crossed that the organisers of the event are going to write down all the work they did to run the event as a contribution to _The Turing Way_. +It was a really really thoughtfully run event, all the way down to a badge making station and personal thank you cards and brain cookies πŸ˜‹πŸ§ πŸ˜‹ + +
+ Card with Kirstie written on the front and brain shaped cookies wrapped in cellophane +
Delicious brain cookies that Kirstie received as a thank you from the organisers of OpenMR Benelux (via Kirstie's twitter feed). +
+
+ +**Yo** shared a call from "[I'm a scientist, get me out of here](https://imascientist.org.uk/scientists/)" for more folks to join them (deadline **27 January**). +It involves chatting with kids about science, its good for fulfilling scicomm requirements in grants, and there's the chance of a prize at the end. + +**Yo** also passed her first year EngD interview! +CONGRATULATIONS from everyone in the lab 🎊 πŸŽ‰ ✨ + +**Patricia** shared that her main realisation this week was how much she enjoyed putting conference submissions together when she has a bit of freedom, some time to think, and good collaborators. +She also shared this article: "Low-carbon, virtual science conference tries to recreate social buzz" (doi: [10.1038/d41586-019-03899-1](https://doi.org/10.1038/d41586-019-03899-1)(doi: 10.1038/d41586-019-03899-1). + +On form as ever, **Kirstie** asked for this to be created as a potential chapter in _The Turing Way_, so now there's a chapter proposal issue: [#803](https://github.com/alan-turing-institute/the-turing-way/issues/803) to collect resources! +If anyone is interested in writing it (or part of it!), that would be wonderful! πŸ’– + +**Elizabeth** is about halfway through ["How to do nothing: Resisting the attention economy"](https://www.penguinrandomhouse.com/books/600671/how-to-do-nothing-by-jenny-odell/). +She's loving it so far. +It's a critique of our cultural insistance that time should be spent "productively". +It also tries to motivate how and why we should work together to to hold open an (emotional, intellectual) space where we refuse that framing, without just dropping out and neglecting our responsibilities to society. + +**Georgia** shared a link to [Women At The Table](https://www.womenatthetable.net) a growing, global gender equality & democracy CSO. + +> "The lifeblood of our world’s decision-making is data. +> And therefore we are at a critical turning point – we must create new norms and write a new data story. +> We must make the data revolution a gender data revolution grounded in human rights." + +Tomorrow **Ang** and **Yini** will celebrate Chinese New Year's Eve. +This is the first time **Ang** has not been in his hometown. +He is missing his family and will make a lot of video calls tomorrow! + +The lab are thinking of everyone affected by the [coronavirus](https://www.theguardian.com/science/2020/jan/25/what-is-the-coronavirus-wuhan-china-virus-symptoms) in the city of Whuan and the surrounding areas. + +**Yini** shared a beautiful picture of the northern lights that she saw last week. + +
+ Green lights in dark sky +
Northern lights from Norway. +
+
+ +**Malvika** gave a talk today at [OpenMR Benelux](https://openmrbenelux.github.io/). +The slides are available at [https://speakerdeck.com/malvikasharan/designing-open-and-inclusive-communities](https://speakerdeck.com/malvikasharan/designing-open-and-inclusive-communities). +She also shared [GitPitch](https://gitpitch.com) which is a tool to show presentation slides from markdown, and [braindr](https://braindr.us/#/) (now extended to [Swipes for Science](https://swipesforscience.org/)) built by the wonderful [Anisha Keshavan](https://anisha.pizza/#/). +You can read all about the genesis of the project, now supported by eLife, in her paper "Combining Citizen Science and Deep Learning to Amplify Expertise in Neuroimaging" (doi: [10.3389/fninf.2019.00029](https://doi.org/10.3389/fninf.2019.00029)). + +**Isla** is applying for jobs at the moment, and has spent lots of time this week cribbing about the linux kernel! + +We discussed in the meeting the particular challenge that interviews hold for introverted people. +It's really tough trying to show off about yourself, in part because that assessment is so wrong! +Also the time pressure to perform in is so wildly different to reality. +Patience & humility are so important in the real world. +We recommended trying to reframing the question away from "showing off" to how you can **help** the organisation achieve its goals. +That might not be what they asked, but it certainly is what they'll be interested to hear. + +We all sent **Isla** a big group hug. +GOOD LUCK πŸ’– + +**Louise** went to a really interesting seminar by [Alan Garfinkel](https://www.lincoln.ox.ac.uk/Fellows/AlanGarfinkel) the other day that focussed on Alan Turing's work on reaction diffusion equations and emergent [pattern formation](https://en.wikipedia.org/wiki/Turing_pattern). +She found it fascinating, especially as there are so many beautiful patterns that simply pop out of the equations πŸ˜„ + +## Questions we're thinking about + +**Kirstie** asked the lab to complete a few sentences about themselves to update the lab's [who's who](/about) page. +She's so proud to be working with such wonderful people 😊 ✨ 😍 + +**Patricia** asked what lab members expect from a session chair at a conference? +What makes a good session chair except keeping to time? + +Some answers included: + +* Thoughtfully managing questions. + The chair should ask a question if no-one volunteers (as is often the case). + If there are multiple people with hands raised then choosing a woman first has tended to result in a more diverse set of question askers than if the first asker is male. +* Introducing speakers with a sentence or two if you know them well enough. +* Asking how to pronounce speaker names _before_ the session! + +**Yo** asked a question that we discussed in detail: how do we each feel about absentee managers / leaders / mentors? + +Some of the lab's comments and experiences included: + +* I used to think "rarely available but nice when around" was fine, but I feel like making an active effort to be hands-on and not always busy is actually pretty important if you want people to feel valued. +* Preparing briefing docs or a clear powerpoint on my work for an overly busy supervisor really helps to get useful input when we did meet. +* Praise is so important, but it has to be real. + Hearing "well done" if there isn't enough trust to believe that my manager actually means it rings hollow. +* One thing I try to do when, say, reviewing a document, is to highlight bits and explain _why_ I liked them, to make the praise seem real-er. +* Having a busy supervisor nudged me to learn to communicate with my colleagues more often. +* It's particularly difficult to know how to make a decision before joining a position. + The job or doctoral project description is so short, and an interview won't give you information on whether your mentor is good or not. +* A major challenge is that these are structural problems in academia. + Spending time supporting students and staff on anything that isn't a co-authored paper is actively disincentivsed by academic reward structure. +* A good phd supervisor at the start of your degree is a bad one at the end, and vice versa. + Its important not to look for everything you need in one person. +* The time scale of impact from mentorship and training is long. + The [mathematics geneology project](https://genealogy.math.ndsu.nodak.edu) and [The Academic Family Tree](https://academictree.org) show if people train others who go on to be successful... in academia only. + These projects don't track success if trainees leave academia 😭 +* Professional services can support you.....but they're often not promoted or enabled. +* Don't look for a specific mentor, build a mentor from LOTS of different people and their strengths. +* If the goals of supervisor and student are not aligned then they could try to design outputs that are going to benefit both. + For example if the student wants to go into industry, they could focus on building infrastructure and pipelines in the lab rather than writing papers. + (Although this can backfire when it comes to the degree requirements - at least at the moment!) + +**Sarah** asked how to encourage people to use a service? +Hub23 (the Turing's private BinderHub) doesn't currently have any users which is a shame because she's put a lot of work into making it really easy for me to maintain (e.g. [writing bots](https://github.com/HelmUpgradeBot) to keep the helm chart up-to-date and the container registry in a manageable state). +It would be so sad to tear it down. + +She's trying to encourage participation by holding hackathons as part of our team collaborative time and it would be good to roll this out to more of the Institute. +**Kirstie** agreed that it needs a little more development first. +Apart from allowing GitHub login it's exactly the same as [mybinder.org](https://mybinder.org/), whereas what people really want or need is to use Binder for private code or data. +The lab also sent some solidarity - its tough to be the only person working on a tool or infrastructure project πŸ€— + +**Georgia** asked for advice on combining (continuous) open source and (continual) agile workflows. +The lab are going to dedicate a future lab meeting to this discussion. + +**Ang** shared a paper: "Alpha Waves as a Neuromarker of Autism Spectrum Disorder: The Challenge of Reproducibility and Heterogeneity" (doi: [10.3389/fnins.2018.00662](https://doi.org/10.3389/fnins.2018.00662)). +He was particularly shocked by figure 4 (below). +**Sarah** recommended [Docker](https://docs.docker.com/engine/docker-overview/) and [Singularity](https://sylabs.io/docs/) as important tools to address this problem. +They're both described in the _Turing Way_ chapter on [Reproducible Environments](https://the-turing-way.netlify.com/reproducible_environments/06/containers.html). +Ultimately though, we need a shift in culture that says sharing code and data is no longer enough for reproducibility, but the computational environment the analysis was performed in also needs to be shared. + +
+ Two scatter plots +
Alpha waves characteristics analyzed by Matlab 2013 versus Matlab 2014. + (A) Alpha peak power (dB). + (B) Alpha frequency (Hz). + From Lefebvre et al, 2018 (doi: 10.3389/fnins.2018.00662). +
+
+ +**Yini** asked the best phrasing to use when a p value of a hypothesis test is greater than 0.05, and how to discriminate between "evidence of absence" and "absence of evidence"? +**Kirstie** answered that ultimately the only thing you can say about a p value greater than alpha (the _a priori_ threshold for assessing statistical significance for this test) is that you accept the null hypothesis: there is no evidence for the relationship you're investigating. +(See this blog post for a [list of 500 ways](https://mchankins.wordpress.com/2013/04/21/still-not-significant-2/) that papers have tried to get around this unfortunate truth. +Don't join their rankings!) +If you want to give *evidence of absence* you'll have to use a [bayesian framework](https://en.wikipedia.org/wiki/Bayesian_inference). +[Alex Etz](https://twitter.com/alxetz) has some [wonderful resources](https://osf.io/846x7/) that he curated for the [Advanced Methods in Reproducible Science](https://osf.io/gupxv/) workshop earlier this year. + +## An open discussion + +Much of the meeting was spent discussing the comments above, particularly **Yo's** question about mentorship and line management, and **Isla's** job interview experiences. + +We wished each other a happy [Year of the Rat](https://chinesenewyear.net/zodiac/rat/) πŸ€. +新年快乐 (xΔ«n niΓ‘n kuΓ i lΓ¨). \ No newline at end of file diff --git a/about/index.md b/about/index.md index 854d34da..e3f0e222 100644 --- a/about/index.md +++ b/about/index.md @@ -8,45 +8,173 @@ excerpt: "Members of the Whitaker lab and their research interests." Kirstie Whitaker +Kirstie Whitaker is a Research Fellow at [The Alan Turing Institute](https://www.turing.ac.uk/) (London, UK). +She completed her PhD in Neuroscience at the University of California, Berkeley in 2012 and holds a BSc in Physics from the University of Bristol and an MSc in Medical Physics from the University of British Columbia. +She joined the Department of Psychiatry at the University of Cambridge in 2012 and conducted her postdoctoral research in the Brain Mapping Unit under the supervision of Professor Ed Bullmore. +She remains a member of the department as a senior research associate. -Kirstie Whitaker is a Research Fellow at [The Alan Turing Institute](https://www.turing.ac.uk/) (London, UK). She completed her PhD in Neuroscience at the University of California, Berkeley in 2012 and holds a BSc in Physics from the University of Bristol and an MSc in Medical Physics from the University of British Columbia. She joined the Department of Psychiatry at the University of Cambridge in 2012 and conducted her postdoctoral research in the Brain Mapping Unit under the supervision of Professor Ed Bullmore. She remains a member of the department as a senior research associate. +Her work covers a broad range of interests and methods, but the driving principle is to improve the lives of neurodivergent people and people with mental health conditions. +Dr Whitaker uses magnetic resonance imaging to study child and adolescent brain development and participatory citizen science to educate non-autistic people about how they can better support autistic friends and colleagues. +She is the lead developer of [*The Turing Way*](https://github.com/alan-turing-institute/the-turing-way), an openly developed educational resource to enable more reproducible data science. +Kirstie is a passionate advocate for making science "open for all" by promoting equity and inclusion for people from diverse backgrounds, and by changing the academic incentive structure to reward collaborative working. -Dr Whitaker uses magnetic resonance images to understand the changes in the brain's structure and function that underlie the emergence of schizophrenia and depression. Her work has shown that changes in myelin content in the brain's "grey matter" increase through adolescence and that association cortex - the area of the brain that underpins complex cognition such as reasoning - continues to develop into your 20s and beyond. +Dr Whitaker is a Fulbright scholarship alumna and was a 2016/17 [Mozilla Fellow for Science](https://science.mozilla.org/programs/fellowships/fellows). +She was chair of the Organization for Human Brain Mapping's Open Science special interest group in 2019 and served on the committee as chair-elect in 2018 and past chair in 2020. +She is founding chair of the Turing Institute's Ethics Advisory Group and member of the Tools, Practices and Systems leadership team. +Kirstie was named, with her collaborator Petra Vertes, as a [2016 Global Thinker](https://gt.foreignpolicy.com/2016/profile/petra-vertes-and-kirstie-whitaker) by Foreign Policy magazine. -Kirstie is particularly passionate about ensuring that work is reproducible and can be replicated in independent data sets. She is committed to supporting early career researchers ensure they can share their data and code while also following strict ethical guidelines. As a researcher at the Turing Institute Dr Whitaker focuses on how data science techniques can improve neuroimaging analyses, including the application of machine learning techniques to big data sets such as UK Biobank. +Her role in the Whitaker lab is to shepherd the incredible team, to build connections to help them work collaboratively and inclusively to efficiently achieve their goals. +In her spare time [she tweets](https://twitter.com/kirstie_j) (a lot) and hangs out with her dog [in Greenwich Park](https://twitter.com/kirstie_j/status/1186900239531331585?s=20) or with her family [in the Lake District](https://twitter.com/kirstie_j/status/1215696702826397696?s=20). -Dr Whitaker is a Fulbright scholarship alumna and was a 2016/17 Mozilla Fellow for Science. She will be the chair of the Organization for Human Brain Mapping's Open Science special interest group in 2019 and is currently serving as chair-elect. Kirstie was named, with her collaborator Petra Vertes, as a 2016 Global Thinker by Foreign Policy magazine. - -__More information:__ +**More information:** * CV: [Whitaker_CV.pdf](https://github.com/WhitakerLab/WhitakerLabProjectManagement/blob/master/weekly-updates/Kirstie-Whitaker/Whitaker_CV.pdf) * GitHub: [@KirstieJane](https://github.com/KirstieJane) * Twitter: [@kirstie_j](https://twitter.com/kirstie_j) +* ORCID: [0000-0001-8498-4059](https://orcid.org/0000-0001-8498-4059) * Email: [kw401@cam.ac.uk](mailto:kw401@cam.ac.uk) or [kwhitaker@turing.ac.uk](mailto:kwhitaker@turing.ac.uk) (both work equally well) -## Research assistants +## Researcher associates + +### Georgia Aitkenhead + +Georgia is a research associate at The Alan Turing Institute. +She works with Kirstie on a participatory science project to build a [citizen science platform](https://github.com/alan-turing-institute/AutisticaCitizenScience) investigating autism and sensory processing. +She loves jazz music, running, poetry. -### Isla Staden +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +### Malvika Sharan -Isla Staden +Malvika is a research associate at the Alan Turing Institute, leading the community management of [_The Turing Way_](https://github.com/alan-turing-institute/the-turing-way) project. +She is interested in developing a better understanding of community building in the intersection of Open Science and inclusiveness. +Her role in the Whitaker Lab is to develop the [_Turing Way_](https://github.com/alan-turing-institute/the-turing-way) project and facilitate an inclusive platform for its community. +In her spare time she tries not to miss her yoga and lindy hop classes, and sometimes can be spotted strumming her ukulele. +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* +## Visiting doctoral students +### Yini He +Yini is a visiting student in the Alan Turing Institute and a PhD student with a major in neuroimaging at the University of Electronic Science and Technology of China (UESTC). +She is working with Kirstie & [Ang](#ang-li) on understanding the relationship between polygenic risk, brain structure and mental health conditions. +Yini loves visiting museums in the spare time because she is really interested in the traditional cultures around the world. +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* -Isla Staden is a Research Assistant in the Whitaker Lab, refactoring [Brain Networks In Python](https://github.com/WhitakerLab/BrainNetworksInPython) and curating data in the [Neuroscience in Psychiatry Network](http://www.nspn.org.uk/). She is interested in topology and network science; open source development; open data and reproducible science and finally brains. +### Ang Li -__More information:__ -* CV: [Isla-Staden-CV.pdf](https://github.com/Islast/WhitakerLabProjectManagement/blob/master/Isla-Staden/Isla-Staden-CV.pdf) -* GitHub: [@Islast](https://github.com/Islast) -* Twitter: [@IslaStaden](https://twitter.com/islastaden) +Ang is a PhD candidate in [Chinese Academy of Sciences](http://english.ia.cas.cn) and a visiting student at the Alan Turing Institute. +He is interested in using multimodal data to study mental health conditions, human consciousness and neurodevelopment. +He works with Kirstie and Yini on a project to understand the impacts of genetic predisposition for schizophrenia on neurodevelopment. +In his spare time, he loves taking photos, listening music and popularization of science. + +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +## Affiliated researchers + +### Sarah Gibson + +Sarah is a Research Software Engineer in the Research Engineering team at The Alan Turing Institute. +Her work involves using software engineering and data science solutions and best practices to solve real world problems and bridge the gap between the cutting edges of academic and industrial research. +Her specialism lies in cloud infrastructure for research reproducibility. +As a member of the Whitaker Lab, Sarah shares her passion for reproducible research and offers guidance on reproducibility tools or best practices, all while learning about a research domain that is completely new to her! +In her spare time, she enjoys music and cross-stitch. + +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +### Patricia Herterich + +Patricia is a Research Data Specialist at the [Digital Curation Centre](http://www.dcc.ac.uk/) at the University of Edinburgh. +She's mainly contributing to the [FAIRsFAIR project]( https://www.fairsfair.eu/) supporting data repositories and research support staff in offering services that facilitate FAIR data. +She's a remote participant in Whitaker lab calls and contributes a support staff perspective on open research topics. +In her spare time, she obsessively listens to podcasts, enjoys jigsaws, crochet, and watching her husband play video games and making and eating vegan food. -## PhD students +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +### Yo Yehudi + +Yo is a Software Developer at the Department of Genetics University of Cambridge and EngD student at the School of Computer Science at the University of Manchester. +In both cases their interests lie in human factors of software engineering - e.g. user experience and usability of software, and open source community management. +They share their extensive expertise in these domains with Whitaker Lab members remotely from Cambridge. +They're very bad at spare time, but likes to read, cook, craft, and bike/hike outdoors, not necessarily in that order. + +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +## Alumni + +### Maxine Mackintosh + +Maxine Mackintosh was a visiting PhD student in the Whitaker lab and an enrichment student at the Alan Turing Institute from September 2018 to August 2019. + +**More information:** +* CV: *delete this row if you don't want to include this information* +* GitHub: *delete this row if you don't want to include this information* +* Twitter: *delete this row if you don't want to include this information* +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* ### Jessie Liu -Jessie Liu is a visiting PhD student in the Whitaker Lab and an enrichment student at the Alan Turing Institute. +Jessie Liu was a visiting PhD student in the Whitaker Lab and an enrichment student at the Alan Turing Institute from September 2017 to August 2018. __More information:__ +* CV: *delete this row if you don't want to include this information* * GitHub: [@lzdh](https://github.com/lzdh) * Twitter: [@lzdhlzdh](https://twitter.com/lzdhlzdh) +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* + +### Isla Staden + +Isla Staden + +Isla Staden was a Research Assistant in the Whitaker Lab, refactoring [Brain Networks In Python](https://github.com/WhitakerLab/BrainNetworksInPython) into [scona](https://github.com/WhitakerLab/scona)πŸͺ and curating data in the [Neuroscience in Psychiatry Network](http://www.nspn.org.uk/) from June 2017 to August 2018. +She is interested in topology and network science; open source development; open data and reproducible science and finally brains. + +Isla remains the lead developer of scona πŸͺ, a Python package to perform `s`tructural `co`variance `n`etwork `a`nalysis of the human brain. +She has a strong interest in the implementation of tools to promote reproducibility of scientific research. +In her spare time Isla plays d&d and roller derby and watches a lot of ballet on youtube. + +__More information:__ +* CV: [Isla-Staden-CV.pdf](https://github.com/Islast/WhitakerLabProjectManagement/blob/master/Isla-Staden/Isla-Staden-CV.pdf) +* GitHub: [@Islast](https://github.com/Islast) +* Twitter: [@IslaStaden](https://twitter.com/islastaden) +* ORCID: *delete this row if you don't want to include this information* +* Email: *delete this row if you don't want to include this information* +