This week, we’re hosting a community call on issues of reproducibility in science, and we want you there! For background, the Science Lab community call takes place every other month, highlighting recent developments and work of the community relevant to science and the web. Join us to hear more about current projects, find out how you can get involved, and listen to others (or yourself!) discuss work in and around open research.
The call is open to the public, starts at 11:00 am ET.
Call in details can be found on the call etherpad (where you can also find notes and the agenda). As with our April call, we’ll feature speakers on Air Mozilla, a video live-streaming platform which will be a departure from our typical dial in, and hopefully more accessible!
For June’s call, we’ll be talking about reproducibility specifically, featuring speakers who build scientific projects and programs that try to improve the reuse, ratification and remix-ability of scientific research progress. Productive open science work depends on reproducible and rigorously tested results, and we’ll tease out some of the factors that influence research reproducibility. You can look forward to hearing from the following group of speakers across research, industry, and institutional domains:
Fatma (Imamoglu) Deniz – developing an e-book for reproducible science, Postdoc, Helen Wills Neuroscience Institute
Ciera Martinez – crowdsourcing a guidebook for reproducible practice @CieraReports, Postdoc, UC Berkeley
Aaron Williams – using evidence to elevate the debate on policy issues @awunderground, Urban Institute
David McClure – collaborating at a non-profit science/society/econ policy research org @clured, Urban Institute
Kristin Ellis – building bio experiment bots w/ open source components @SexyLikeMeiosis, Open Trons
Michael Markie – developing immediate + transparent publishing for science @mmmarksman, F1000 Research
We’ll also hear our closing updates from our 2016 Mozilla Fellows for Science, and our 2017 Global Sprint participants, as well as more updates on our 2017 Fellowship Applications, our Mini-grants + Mozfest CFPs, and our Book Club! Should be a great call!
Have an update, blog post or event you’d like to share relevant to open science? Add it to the etherpad (see ‘Non Verbal Updates’). It’s a great way to share what you’re working on and/or interested in with the community. Don’t be shy. Have a look at last month’s notes on trust in open science for an idea of what others contributed to the conversation.
Mark your calendars, tune in and help us spread the word – everyone is welcome. For call-in details and links to the etherpad, visit our wiki page. We hope you’ll join us!
Paul (@paulvilloutreix) is a Postdoctoral Fellow at Princeton University and a Visiting Fellow at the Center for Data Arts at The New School. I met Paul at our Working Open Workshop in Montreal where I was blown away at how he combines design, science and technology in his project, The Embryo Digital Atlas.
I interviewed Paul to learn more about the Embryo Digital Atlas and how you can contribute June 1–2 at #mozsprint.
What is The Embryo Digital Atlas?
The Embryo Digital Atlas is an open source web based platform to visualize complex experimental datasets of embryogenesis in an easy and beautiful way. Embryogenesis is the process by which a single fertilized egg is transformed into a multicellular organism. It is studied in various model organisms, from the sea urchin, to the fruit fly, to the zebrafish, to the chicken, to the mouse, to the human! Many mechanisms are conserved across species, this is why it is useful to study and compare this process in the various models. Imaging studies play a big part in these studies, mainly because this is such a complex and intricate process that researchers first need to be able to describe it comprehensively.
Embryogenesis is at the heart of the public debate about stem cell research or genome editing. In addition, it is a source of inspiration for engineers, designers and architects interested in how a complex structure can emerge from simple units. The aim of The Embryo Digital Atlas is to make public datasets of embryogenesis easily accessible for an audience ranging from curious citizen, to students, to professional researchers.
Why did you start The Embryo Digital Atlas?
While working with experimental biologists at Princeton University, I started noticing that there were many datasets of embryogenesis that were sitting in the labs and were not necessarily published because they were not associated to positive results. I thought that they could be useful as public resources for the general understanding of embryogenesis.
At the same time, I was playing with some image datasets and found that the current visualization tools were either too generic or required a lot of expert knowledge. To find ways of making scientific image datasets easily and interactively accessible, I started to collaborate with designers and artists at the Center for Data Arts at The New School, leading to The Embryo Digital Atlas project.
Why is it important to be able to visualize embryogenesis?
Embryogenesis is a very complicated process. It involves an enormous amount of variables that need to monitored at the same time to just begin to understand what the correlations between all the processes are. It involves 3D changes in shape that can be challenging to interpret if you cannot interact with the data. Microscopes keep improving, bringing more information, resolution and larger datasets. The study of embryogenesis currently revolves around visualizations. We are at this stage in the field where most of the scientific evidence is based on images.
What problems have you run into while working on this project?
As project lead, the main difficulty is designing specific short term problems and issues that can be solved while maintaining a working prototype and having a project that is consistent with long term goals.
We started developing the platform in JavaScript using the library three.js which implements WebGL. This library is really user friendly and we could quickly have a support for drawing images that can be moved in a 3D space while handling most of the user interactions. The current datasets are relatively small, about 30–40 MB. One problem that we are currently facing is how to visualize much larger datasets, from 10 GB to a few TB.
Later on we would like to combine this visualization tool to an image storage platform. The Open Microscopy Environment is a great community developing open source software which should be very useful for this part of the project. Other future developments involve collaborative annotation of the datasets or using Virtual Reality to explore immersive approaches to scientific data visualization.
What kind of skills do I need to help you?
My main goal at the Mozilla Global Sprint is to set up an operational website, with a nice overall interface,smooth navigation,content that is well organized among the pages and some nice features such as animations during loading times. I am looking for anyone with skills in user interface and web design who would like to contribute to a cool science project!
How can others join your project at #mozsprint 2017?
A few easy things that could be very helpful to start with are contributions to the layout, particularly the implementation of the header, footer, tabs and navigation. It could also be great if the layout would be adaptable to tablets and smartphones with smaller screens. That requires some knowledge in html, css, and php and some design skills.
The project is currently on my personal github — https://github.com/paulvill/paulvill.github.io. There is a list of issues which is maintained up-to-date on the github repository, so do not hesitate to jump on any where you think you can contribute.
I can be reached on twitter at @paulvilloutreix or by email at paul.villoutreix@gmail.com
“There is perhaps no better demonstration of the folly of human conceits than this distant image of our tiny world. To me, it underscores our responsibility to deal more kindly with one another, and to preserve and cherish the pale blue dot, the only home we’ve ever known.” ~ Carl Sagan, Pale Blue Dot: A Vision of the Human Future in Space
In this post I tell the (long) story of how I found out about Mozilla’s work in Science; how I became a fellow; and what this experience has been like. I’ve also included my last year application, hoping that it will help new applicants get some inspiration. I highly recommend this fellowship to anyone that loves (Open) Science!!! Don’t forget the deadline for this year applications is this Sunday (May 14th)!
The Mozilla GLOBAL SPRINT is just over three weeks away – Thursday and Friday, June 1-2, 2017.
This is our fourth global sprint but the first one being hosted by programs across Mozilla and not just the Science Lab.
Since we have so many new folks participating, we wanted to share some answers to frequently asked questions to help you get started.
When is the sprint taking place?
June 1-2, 2017
Sites around the world will be open for participants to come by and work on open science projects.
Each site will be open during some portion of normal business hours (usually around 9:00 am to 5:00 pm local time).
Sites will keep posted hours — no all-nighters, please — and each site will wrap up by the end of regular business hours on Friday, June 2.
Brisbane & Melbourne, Australia will be the first 2 sites live (UTC + 10), with additional sites coming online at the start of their Thursday.
What projects are currently included in the sprint?
A list of featured projects can be found here under “Projects”
This year we’re hosting demo calls ahead of time so you can learn about the projects that will be available for collaboration during the sprint. You can read about upcoming calls and hear past recordings.
We have five tracks this year on issues related to Internet health:
Head here for a full list of projects promoting internet health that will be a part of this #mozsprint.
Do I need to be a programmer?
No – the sprint is designed for all kinds of participants, including researchers, developers, educators and open web enthusiasts. There are a host of projects with something for everyone to help with, from reviewing code or lesson/documentation content, to helping create curriculum, design graphics and even hack on tools. Take a look at the projects linked above to find out the many ways that you can contribute.
Do I need to register somewhere?
Yes, please! Check out our Site Map – to find a site closest to you and click on the site location link below the map to register for a free “ticket” for that location.
Can’t find a site that’s close? Register as a “Virtual Participant”.
What sites are currently included?
There are sites all around the world. An up-to-date list of active sites is posted here.
Do I have to be at one of the listed sites?
Not at all — many people will be available to help out and answer questions online via web conferencing, IRC, Gitter chat room and Twitter. Read the documentation for each project for preferred communication methods. But if you can get to one of the listed sites, it would be a chance to make some new friends.
Where are those sites, exactly?
Addresses and maps along with site-specific information can be found on each of the sites listed on our Site map.
How will sites be connected?
We will set up a single Vidyo web conference room to connect all of the active sites and participants, primarily to give people a sense of who’s awake where.
We’ll be using a Gitter chat room to answer questions and for discussions across participants and of course Twitter.
If I can’t make it to a site how can I participate remotely?
Join the Vidyo conference room any time during the two-day sprint to connect with project leads, sprint participants and site hosts. To join the conference follow the installation instructions here and join us during your regular working hours. To stay up-to-date on notifications about the sprint Register here as a Virtual Participant.
Where will work take place online?
Each project will use the version control (Github) repository, issues lists, and so on that it usually uses to manage participant contributions. Some may be a little different – just ask the project lead how they’d like you to participate. Details on how to participate in a specific project are provided in their Github repository – all projects are listed here.
How can I make contact with a project I’m interested in?
The names of the project leads are listed in each of the project issues – add a comment to the project issue at the bottom indicating that you are interested and the project lead will get in touch to discuss how you can contribute to their project.
If you still need more information … head to the GitHub repository for the project, the link will be inside each issue and take a look at the README.md and/or CONTRIBUTE.md for guidelines on how to contribute ELSE follow any additional links posted by the project lead.
What should I do to prepare?
Register either at a specific site or as a virtual participant here.
Decide which project you’d like to work on. (We recommend that people focus on just one—two days goes by very quickly.) – all projects are listed here.
Head over to the project Github repository.
Have a look at the project’s open issues to find something to start working on.
Show up during open times for your site (usually around 9:00 am local time).
Introduce yourself to the site host and/or the person coordinating the project you’re working on if they are at that site.
Check your chosen project’s issue list and/or chat with the coordinator to see what needs to be reviewed. (Reviewing is often a gentler way to ease into work than writing or coding.)
Once you’ve done a review or two, pick some writing, drawing, or coding that needs to be done, check to make sure no-one else is already doing it, and dive in.
Repeat until it’s time to wrap up for the day, then get a good night’s sleep and come back in the next day to do it again.
Do I need to bring my own computer?
Yes, please. Machines will not be provided.
Do I have to be there on both days?
No, feel free to participate as long as you can. It is helpful for people to commit to at least one full day (or two half-days) so that projects don’t spend all of their time getting newcomers on board.
What about coffee, lunch, and dinner?
We suggest that the sites provide coffee (and snacks if they can), but do not need to provide meals. That said, we strongly encourage the people working at each site to get lunch together, and to go out together at the end of the first day: this sprint is meant to help build community, and sharing a meal with someone is a great way to get to know them.
tl;dr: Apply today. It will change your life (even if you aren’t selected!) Deadline: 14th May
My Mozilla Fellowship Journey
I first heard about the Mozilla fellows for science program in 2015. My first, and only, response was “This was made for me”!
When I finished my PhD in Neuroscience from the University of California at Berkeley, I was so frustrated with the academic reward system. Specifically, I had found many null results during the five years of my PhD, and I had also failed to replicate some already published findings. I knew others had had the same experience, but we weren’t writing up our efforts, we kept going back to the drawing board to find sufficiently novel and significant results so we could graduate.
I didn’t want to give up on doing science for a career though. A good day in science – where you get to talk with super smart and thoughtful people about how the brain works, develops, learns and evolves, is one of the very best ways to spend your time. The problem is simply that so many of these smart people leave academia to a) be paid more, b) maintain a better work-life balance, and c) have clearer goals and expectations.
Mozilla Science lab is investing in the future of science. The fellowship, and the associated community, has brought me hope and inspiration to support the next generation of scientists. People who collaborate rather than compete, who accept that we make mistakes and that our theories evolve, and who believe that by sharing our work we can build something so much better that we each could create alone.
In this blog post I’m going to talk you through my application journey. Please reach out (I’m @kirstie_j on twitter) if you have any questions or comments.
My first – unsuccessful – MozFellows application
I submitted my 2015 application while I was on holiday in Edinburgh with friends. Hiking up Arthur’s Seat the following (very windy) day felt really great.
Celebrating my first Mozilla fellowship application with a windy hike in Edinburgh
I didn’t end up being chosen, but I was still really inspired to join a community I felt were able to make a difference in the lives of early career researchers around the world.
This is my answer to the question “Why is the open web important to you?”, from my 2015 application:
The open web is the great equaliser. It doesn’t matter where you come from, your gender, sexual orientation or race: the open web allows you to meet peers, mentors, role models and friends. Academia is competitive and, sometimes, dangerously isolating. The mental health challenges for highly educated “trainees” is often not appreciated by those in power and the “crushing self-doubt” of the imposter complex pervades our halls. The open web allows science to advance by sharing our deeper understandings (rather than only the novel or unexpected results) and by supporting the real human beings who undertake those analyses every day.
MozFest 2015
I’m not going to lie, I was pretty nervous heading to MozFest in November 2015. I knew I should go – I don’t live far from London and it was going to be an excellent weekend event – but I was also going to have to be brave and meet the four successful fellows without appearing too jealous! 😒
Fortunately, it was easy. The atmosphere at MozFest was enthusiastic and friendly. I partly blended in with the crowd and partly chatted with lovely people. I immediately felt like I’d joined a community of like-minded friends.
My fortune cookie even supported my life view that file organisation is super freaking important!
My MozFest 2015 fortune
The workshops in the Open Science space were amazing. My favourite was Pull Request bingo lead by Mu-An Chiou. (That was my very first experience with collaborating via GitHub!)
Working Open Workshop in Berlin, February 2016 and Open Leadership Cohort mentorship
The coolest part of being rejected from the Mozilla Fellowship program in 2015 was being invited to their very first Working Open Workshop in February 2016.
It was outstanding. I met the other 30 members of the Open Leadership Cohort and we all supported each other in developing our projects. I brought with me the STEMM Role Models project which had just been selected as finalist for the Rosalind Franklin appathon.
At the Berlin WOW I build up our project’s GitHub repository. We learned about the importance of welcoming people to your project (the almighty README.md welcome mat), giving clear guidelines on how to contribute (CONTRIBUTING) and on community norms (CODE_OF_CONDUCT).
After I came home from Berlin I had fortnightly meetings with Abby and Aurelia – my Mozilla Science lab mentors – who held my hand and supported me all the way through to the Global Sprint….where the STEMM Role Models team of contributors made our very first website and database! Meeeep! 😍✨🎉
MozFest Retreat in Berlin, May 2016
In May 2016 I was invited to help out organising (wrangling) the Open Science space at MozFest 2016. The three day retreat in Berlin with Arliss, Joey and Richard, along with the other Mozilla space wranglers was exceptional.
We spent three days talking about our hopes and dreams for MozFest. We were completely focused on building an event that could bring together advocates for the open web, and support Mozilla’s mission to ensure that everyone has access to this incredible resource.
I’d never seen so many postit notes before that retreat, but I have since! I’m completely sold on the benefits of staying up above the nitty-gritty and thinking big. Focusing on our shared goals let us develop the biggest MozFest to date, and I’ve tried to bring some of the meeting management techniques from the retreat to project meetings for my other collaborations.
Our postit board from discussions at the MozFest retreat in Berlin
My second – successful 🎉 – MozFellows application
One year later, here I was, ready to submit a second Mozilla Fellowship application. I had built up some incredible experiences and I had a project that showed my dedication to working open. That didn’t mean I was a sure thing by any means, but I knew that there was no downside to trying again.
Here’s my answer to the question “What do you think needs to change most immediately in scientific research?”:
We must incentivise the measurement of the reproducibility and replicability of scientific findings. We should preregister our analyses, publish null results and ensure that researchers are rewarded for rigour rather than novelty. The scientific method is defined by the constant testing, updating and integration of previously acquired knowledge and it is essential we return to that philosophy. At a minimum, raw data, analysis code and instructions to recreate figures need to be made available to reviewers with all submitted journal articles. More extensively, we must better reward the people who build, develop and document tools to facilitate this process.
I again had three sets of interviews, and my supervisor was even interviewed to check that he was supportive of spending my time as a Mozilla fellow for science. Everyone was really great (again) and I was over the moon when I received an email from Aurelia with the subject line: 2016 Mozilla Fellowships for Science: Congratulations!
The congratulations cupcake that my lovely boyfriend bought for me when I was selected to be Mozilla fellow for science in August 2016
The whirlwind that has been the last 9 months
This post is already too long, so I’m just going to bullet point some of the adventures that I’ve had as Mozilla Fellow for Science.
This blog post is so close to this year’s deadline (14th May) because I find it so hard to put into words how much my membership of the Mozilla Science community has changed my life.
I’ve made friends
I’ve been mentored
I’ve mentored others
I’ve laughed
I’ve cried
I’ve felt overwhelmed
I’ve felt inspired
We can do this.
We are the future of science. You are the future of science. Don’t let anyone tell you that there are games you have to play because “that’s the way it works”.
Be the change you want to see in the world, and let all the wonderful folk at the Mozilla Science lab help you on that journey!
2016 Mozilla fellows for science and open web fellows at their onboarding in Toronto. Picture stolen from Aurelia’s post Seeking Open Science Fellows on Medium
“This book is full of gems…lessons from internet experiments in collective intelligence with deep thought about how they apply to the future of what Nielsen calls Networked Science…Highly recommended ” — Tim O’Reilly, founder and CEO of O’Reilly Media
Mozilla’s mission is to ensure the Internet is a global public resource, open and accessible to all. Our global network of technologists, thinkers and builders work for a healthier Internet through core issues like: privacy and security, open innovation, decentralization, web literacy, and digital inclusion. Mozilla stands at the center of a complex web of people around the world, our focus for is to connect more people to each other to take action on Internet health.
The Mozilla Science Lab seeks to identify, support and develop a community of leaders in the network with the aim to transform research and the culture around science to make it more accessible, transparent, and reproducible. MSL specifically focuses on making publicly funded research more open, collaborative, and beneficial by maximizing access and contribution to papers, data, code, and materials. We work to remove barriers -lack of familiarity with tools, skills gaps, and isolation – to make it easier for individuals and communities to make the leap to open practice.
Purpose of the Grant Program
Bridging the gap between early adopters of open science and the many scientists who value, but don’t have time to invest in learning about open is key to moving from science to open science. The 2017 MSL mini grant program invites applicants to submit project ideas that foster innovation and ultimately lead to more robust prototypes and products by expanding and enhancing the community of scientists who are working open. Supported projects will focus on one or more of the following:
Prototyping – Building tools or documentation collaboratively with others. This can be open source code, documentation, tools and technologies used in data-driven science, scientific software, discovery tools (e.g., ways of searching code, hosting services, etc.)
Community Building – These might include mentorship programs, workshops, meet-ups or other events that promote community engagement.
Curriculum – Materials might include text, visuals, and video for online or in-person training.
All projects should specifically reflect priorities that enhance our broader community efforts toward open innovation, efficiency in regards to practicing open science (lower barriers, ease of use & integration, etc), and reproducibility (transparent research methods & results).
Eligibility Criteria
Open to all individuals regardless of geographic location or institutional affiliation.
All materials must be open source, shared under a Creative Commons license of CC-0 or CC-BY, when licensing is required.
Proposals must address one of three key areas: Prototyping, Community Building, or Curriculum. The brief application will require that they reflect an understanding of the work we are currently doing and articulate their own efforts within the needs of the broader community.
Guidelines/Instructions
Grant awards will range from $2,000 – $5,000 USD.
Grant-funded projects or activities should take place between July 1, 2017 and June 30, 2018.
Applications may be submitted for projects lasting up to 12 months.
Final reports will be due 30 days after the end of the proposed project period.
Deadline for entries will be Friday, June 2nd, 2017.
Selection will take place in time for award announcement by July 30th, 2017.
The Mozilla Science Team staff and our advisors will review applications and evaluate them according to guidelines reflecting priorities that enhance the broader community efforts for innovation, efficiency in regards to practicing open science (lower barriers, ease of use & integration, etc), and reproducibility (transparent research methods & results).
Not funded
MSL mini grants cannot be used to support:
Political campaigns and lobbying activities.
Fundraising activities
scholarships or tuition assistance.
These grants are made possible through the generous support of the Alfred P. Sloan Foundation; awardees should provide acknowledgement of the support of Mozilla and the Alfred P. Sloan Foundation in any events or materials produced using grant funds.
Each month, we feature an update from a Study Group Lead. This month we hear from Francesca Mancini (@frances_mancini on Twitter) who manages the Aberdeen Study Group in Aberdeen, Scotland.
On April 5-7th, 2017, the Research Data Alliance (RDA) hosted their 9th plenary meeting in partnership with the Barcelona Supercomputing Center-Centro Nacional de Supercomputación (BSC-CNS). Over the two days, participants attended and hosting working and interest group meetings to evolve research data standards and compose recommendations for more reproducible, interoperable, and legible data management in open scientific research, and the Mozilla Science Lab was in attendance to support and document!
Read on to learn what more and sign up for the next RDA plenary to get involved!
