Our Open Life Science program is based on the Mozilla Open Leader program. Mozilla Open Leaders started 3.5 years ago to make openness the norm in innovation and research. We went through the rounds to find projects that would fit in our program, share them with you and show you the diversity of possibilities.
Galaxy Training Material - Bérénice Batut
The development of genome sequencing has lead to an explosion of biological datasets. The primary problem with these datasets is not the data itself, not computational resources, and not the required storage space, but the lack of trained and skilled researchers to manipulate and analyze this data. Solving this problem requires the development of comprehensive educational resources and the training of researchers. With the support of Galaxy community, we launched a project, the Galaxy Training Material (https://training.galaxyproject.org/), to develop a community-driven framework that enables modern, interactive teaching of data analytics in life sciences and facilitates the development of training materials. The result is a collection of online training materials (>80 tutorials, 77 example workflows, 33 interactive tours), developed and maintained by the worldwide Galaxy community (>80 contributors). These materials are used to support both self-directed learning and giving training courses on bioinformatics analyses using Galaxy, an open data integration and analysis platform for the life sciences.
I aim to build educational materials and project template resources that facilitate researchers, including novice programmer and researchers rushing toward a prototype tools to take steps toward open source best practices. This is motivated both by my own experiences struggling to get my code to a ‘good enough’ point for release and teaching my research assistants to do so and questions from learners at Carpentries workshops I’ve taught on what to do next. Often people learn the fundamentals of programming, but not of packaging or documenting code. This python and ML/data science catered curriculum and templates will facilitate that. (a better name may happen)
Data Science for All - Shadab Hussain
A open Data Science Community, where in experts will train novices, and collaboratively we will work to solve data science problems.
The present project aims to promote inclusive STEM education & to create (not existing) consistence & compact tactile educational material (Workbooks & 3D prints) on Biology & Astronomy. Although there are a few Graphic Libraries for swell papers (e.g. https://tactilelibrary.com & https://imagelibrary.aph.org/aphb/), there is no a compact tactile educational material, such a Workbook. Students’ will “”learn through making”” (Resnick 2017) taking the lead on developing their own ideas in a learning friendly environment (UNESCO 2015). Students will be asked to work at groups of 2s or 3s in order to create a model/draw. Using our laptops & software the model/draws will be ‘convert’ in vector files and 3D source files. These files will be integrated to tactile Workbooks and the 3D prints.During the Workshops we want the teams to work collaboratively on projects, rely on their passions, in playful spirit (Resnick 2017). The project, by engaging children with Science while having fun, will give us the opportunity to bring to the center of attention children with special educational needs and/or disabilities taking the lead in actions and -moreover- a context where children can develop social skills, make friends (Panagiotidou 2016) and ‘learning through making’ (Resnick 2017).
Rapid Reviews for Outbreak Science - Michael Johansson
Based on experiences in the H1N1 influenza, chikungunya, Ebola, and Zika epidemics, we founded Outbreak Science (https://outbreakscience.org/) to improve the use of science to fight epidemics by driving early and open dissemination of data, code, and analytical results. We identified preprints, manuscripts shared publicly prior to peer review, as a key opportunity to share data, methods, and results months before peer-reviewed manuscripts (https://doi.org/10.1371/journal.pmed.1002549). However, preprints also bring new challenges as they can contain important scientific information but also opinions or erroneous research. We thus need ways to rapidly filter preprints so that scientists, policy makers, and lay readers alike can quickly identify the most important scientific information.Through discussions with scientists and policy makers, we identified the need for a tool for rapid, structured, open scientific reviews (very early prototype: https://t.co/acDeHAyHI3). This tool can leverage the broad scientific engagement that occurs during outbreaks. Scientists who read preprints can rapidly provide high-level assessment in minutes rather than the hours that formal peer review requires. And those reviews can be shared immediately and openly unlike most peer reviews. The context of outbreaks is particularly important, but this tool should have much broader potential use, across science and possibly beyond. Open development is thus not just a way to support development, but also key to ensuring that the tool is sufficiently adaptable to be used more broadly.
Open Collaborations: From Local Contributions To Global Recognition - Valentin Danchev
This project will develop an application of blockchain for scientific collaboration with the goal of minimizing gender and status biases in collaborative research, thereby fostering open distributed collaboration. In many online communities, professional sport, and online kitchens nowadays, individual contributions and exchanges are openly available and can easily translate into globally recognizable reputations. In science, however, the very process of doing research collaboratively remains a relatively closed system. By design, local individual contributions and collaborative transactions are not transparently demarcated, possibly contributing to gender and status inequalities as well as to “the rich get richer” dynamics. This project will prototype an open source platform that integrates distributed scientific contributions among collaborators, from ideation to outcome, based on blockchain technology. By designing a blockchain implementation that assembles traceable bits of contributions necessary for assigning credit on the basis of performance instead of status signals, I want to contribute to a more open, inclusive, and reproducible collaborative research.
Science Communication Magazine - Maria Bonatelli
I always had the concern about how to impact and inspire other people to do Science Communication, even though I understand that the main pressure that undergrad and graduate students suffer in university is to publish papers in high impact magazines. But maybe a way to stimulate them to do SciComm is if this production could have a similar value to a scientific paper. Any student that have the desire to share their research to the non-specialized public should be able to do it. But since students are not usually trained to produce SciComm articles, we will offer an online course to capacitate them to produce SciComm article. After, they will send us their article and a group of specialized volunteers will evaluate it. In the end, we will have a quality SciComm product publish in a Magazine that will also have great value to the student curriculum.
Swipes for Science - Anisha Keshavan
I have built a few citizen science games that have proven useful for my research. The breakthrough I had was optimizing my app for mobile. Inspired by Tinder, in braindr (brain data review, https://braindr.us) , you swipe left to fail, or right to pass, the quality of a brain MRI scan. In whaledr (https://whale-dr.firebaseapp.com), you see a spectrogram and hear a 5 second clip of an underwater ocean recording, and swipe right if you hear a whale call.
Openscapes - Julia Stewart Lowndes
Openscapes will help increase the value and practice of open data science in environmental science. Building off of five years of work with the Ocean Health Index (ohi-science.org), Openscapes will focus on engagement and guidance, to excite and connect researchers to existing open tools and communities that can amplify their research.
OpenScienceKE - Caleb Kibet
This project seeks to sensitize and promote open and reproducible Bioinformatics research within Nairobi, Kenya. The current stage of the project involves collaborative writing and community building.
MBac - Computer vision tool for bacterial motility assays - Alexander Kutschera
Bacterial surface colonization and biofilm formation depends on motility in surface environments. Therefore studying bacterial motility is very important to better understand bacterial virulence and persistence. Unfortunately setups vary quite a lot and the reproducibility of bacterial motility assays is comparatively low. For this reason I want to develop an open source imaging setup and computer vision based software to perform and analyse bacterial motility assays!
The Open Reflectometry Project - Diogo Aguiam
Reflectometry researchers must understand plasma physics, microwave propagation, RF electronics and data processing; taking months to years browsing publications and dissertations, before becoming productive. The Open Reflectometry Project aims i) to facilitate the knowledge transfer and collaboration between reflectometry researchers; ii) to educate plasma physicists and engineers that use reflectometry data; iii) and to improve the transparency and reliability of reflectometry diagnostic data.
This project propose to translate the open research outputs in agriculture to local languages like Amharic and also making the translation of the scientific terms to everyday language that the farmers can understand. The translations will be openly available using an online platform to farmers and also to the public so that it facilitates citizen engagement in open science including data collection and data analysis which will promote citizen science to increase agricultural productivity.
PhyloProfile - Ngoc-Vinh Tran
In Evolutionary Biology, the presence/absence pattern of a gene over a set of species is called its “phylogenetic profile”. Phylogenetic profiling is a technique for finding the biological relationships between genes. Due to the uninformative of the basic profile, I am developing PhyloProfile, a visualization method that allows to enrich regular profiles with further data, to make phylogenetic profiling more meaningful. PhyloProfile is open source written in R, making heavy use of Shiny library.
Many fields of science are far behind adopting open scientific practices (e.g. share code). I believe these will be a requirement for publication in the future. However, one of the biggest challenges for many researchers/scientists is that it’s not (at this point) easy to do these practices. This toolkit will simplify and automate many of these tasks. I have already started work on this software project with prodigenr (https://github.com/lwjohnst86/prodigenr).
ContextExplorer: Analysis of organized cell behavior - Joel Ostblom
I want to understand mammalian development and contribute to regenerative medicine cell therapies against currently untreatable diseases. As part of my PhD project, I am using Python and Qt to develop a GUI-driven image data processing application to help biologists study organized cellular behavior in this context in a quantitative manner. These analysis methods are currently not accessible to scientists without a programming background, which is hindering widespread study of these biological processes.
IGNITE - Gracielle Higino
This project aims to put up a training and incentive program in Science Communication to young scientists. The first step would be to gather information about scientists’ needs and worries when they are asked to do SciComm. The next step will be to put up (fun and not much time consuming) training modules focused on these information. We will also look for international applications for funding, so we could offer a fellowship for the trainees or a prize in a contest at the end of the training.
ME-BIDS - Elizabeth DuPre
Functional magnetic resonance imaging (fMRI) is a widely used tool providing a non-invasive, high-resolution index of brain activity. Recently, the Brain Imaging Data Structure (BIDS) was introduced to standardize fMRI data sets, enabling data discovery and—through associated BIDS Apps—analysis. A remaining challenge of fMRI data is its sensitivity to artifacts. Multi-echo analysis (Kundu et al., 2011, NeuroImage) was developed to address this; however, no multi-echo BIDS App currently exists.
Phinch is a open source browser-based, interactive data visualization tool for exploring environmental genomics datasets that enables rapid scientific visualization during the typical scientific research workflow. The project is a collaboration between Dr. Holly Bik (Assistant Professor at UC Riverside) and Pitch Interactive (a data visualization studio in Oakland, CA), and is funded by the Alfred P. Sloan Foundation. End users include reserachers, educators, students, and citizen scientists.
StoryEngine - Christine Prefontaine & Alecia Kuhl
StoryEngine is an impact narrative method that can be used for research, evaluation/assessments, and grant reporting – all the while creating useful communication/marketing/onboarding/network-building assets for both participants and the organization. It is unique because it is open, adaptable, and seeks to provide value to participants (many similar methods are extractive, never giving back to interviewees).
Digital Safety for Open Researchers - Verletta Kern, Beth Lytle, Elliott Stevens, Madison Sullivan & Madeline Mundt
Digital safety is a new and evolving issue in academia. Scholars who wish to work openly do not have time to investigate the topic in addition to their already full teaching and research schedules. Few online resources exist to address these issues in an academic context. We hope to empower researchers/instructors to take charge of their own digital safety through the creation of an online toolkit that can be used at point of need and incorporated into higher education coursework.
Our project aims to disseminate open source practices among high school teachers by co-prototyping with them an open air quality monitor, publishing open air quality data they can reuse with students and documenting the experience in an OER kit. We want teachers to experience the potential that open practices have to address local community issues. Teachers can play a key role in influencing students towards local social innovation, but most of them feel ‘outdated’ regarding ICTs.
FlyCAGE - Basheer Becerra
FlyCAGE is a web application that allow users to search for genes in fruit flies that follow a specific expression pattern. The user can either enter a known gene name to find other genes with similar expression profiles, or the user can enter a custom expression pattern based on experimental data to find genes that follow the pattern. FlyCAGE would be useful in identifying candidate genes involved in a given process and discovering regulatory interactions in genetic networks.
Open Stories - Chealsye Bowley
Open Stories aims to gather success stories of Open advocates and practitioners to show that a successful Open career is possible. Many researchers view Open as a potential risk and they may not see their fields represented in well-known Open advocates. By collecting Open success stories and making them discoverable by storyteller location, discipline, career level, and language, we can better represent the success stories of open practitioners and encourage other researchers to go Open.
Open Yeast Engineering Project (OYEP) - Timothy Stiles
Would you drink a GMO beer? What if you brewed it yourself? The open yeast engineering project (OYEP) at BosLab is an open-ended exploration into yeast engineering. We get together, run experiments, do analyses, and engineer yeast strains to produce flavors, fragrances, and small molecules with the hopes of dextinctifying forgotten flavors or using some resultant strains to produce glowing banana flavored chocolate stout and artificial rosé.
OpenHeart Project - Jo Pauls
The OpenHeart Project aims to improve research practices within the field of mechanical circulatory support (MCS) to improve quality of life for heart failure patients. We aim to promote collaboration and standardization through an open-source research platform. Furthermore, we aim to leverage the existing resources and expertise to develop new and improved solutions for MCS. Through development of online curricula and training tools we aim to improve education and training of researcher.
Brain Networks in Python - Isla Staden
The Brain Networks in Python project seeks to provide open source, documented, tested and modular code to investigate the brain as a network. These analyses are reproducible, transparent and accessible to new and expert brain imaging researchers and network neuroscientists. Openly developed, this project will welcome users and contributors from all disciplines.
Camoco - the co-analysis of molecular components - Rob Schaefer
Camoco is a open source python tool that uses techniques developed from social networks to help biological researchers understand what genes do.
Code Is Science - Yo Yehudi
My project aims to increase awareness of the importance of open source code in science - like all science, code too should be subject to peer review. I would like to conduct research into why code isn’t treated as peer-reviewable science, and curate relevant resources from related open science/open source efforts. This would probably come in the form of interactive workshops and an online survey, with all results shared openly on the project website & hopefully published in scientific journals
Digital Infrastructure for Open Science Hardware - Tobias Wenzel
Open Science Hardware is a new field in Open Science and integral part of Open Innovation. Education and experimental sciences are inherently dependent on instrumentation which becomes increasingly digital and shareable. Yet, open hardware faces many challenges around documentation, sharing and replication that are different from open source software! DocuBricks and the Journal of Open Hardware are open, digital (scientific) infrastructure projects aiming to close the gap!
HBASet: Polygenic expression maps of the brain - Derek Howard
The HBASet project will develop an online, web browser based portal for creating molecular maps of where and when gene sets are expressed in the mouse, monkey and human brains. The tool will take a gene set as input and output interactive visualizations and statistical tests showing the enrichment of expression at a specific developmental time point, brain region, cell type and species. The tool will simplify the examination of expression patterns of a set of genes (polygenic) in the brain.
How does research treat underrepresented minorities? - Athina Tzovara
Most of the existing studies in medicine or psychology are governed by a divide between researchers and participants. Very often, research is focused on underrepresented minority groups, but without explicitly taking their needs and feedback into account. In this project, we plan to collectively design a questionnaire that will be addressed to vulnerable populations and will assess how these populations perceive research done on them.
Mental Hues - Erin Cole
I want to create an open source web application that addresses stigma associated with mental illness. Mental health issues can be viewed on a spectrum. With this in mind, I want users of Mental Hues to be able to create a Hue, or topic, related to mental health. When a Hue has been created, users can write a story related to the Hue to share their experiences. I believe the best way to diminish stigma is to personalize the issues and allow people to relate to them.
Open graduation classes - Felipe Do Espirito Santo
Since last year I’ve started working with open practices with my web design students. We are planning this year to bring our classes to Github and the students can share improvements on the materials, examples and the classes contents after we end each class (they will learn about Git, how to contribute with open source, versioning and stuff like that during that process).
Data Sharing in Neuroscience - Sara Mahallati
To find ways to integrate different data sharing approaches
BrainBox - Katja Heuer & Roberto Toro
BrainBox is a Web co-editing platform that facilitates crowdsourcing neuroimaging data with real-time interactive annotation and segmentation. BrainBox currently provides access to >13k brain imaging datasets. Similar to Wikipedia or Google Docs, it facilitates the creation of distributed teams of researchers collaborating in the analysis of open data – promoting a community effort instead of competition.
Journal Club Starter Kit - Samantha Hindle
Preprint Journal Club Starter Kit is a project to develop resources to encourage the incorporation of preprints into journal clubs (JCs) at research institutions around the world. Preprints are free and immediately available versions of scientific manuscripts that have not yet undergone peer review. By encouraging the reading and evaluation of preprints among groups of scientists, we hope to increase the awareness, usage, and value of preprints, particularly in the biological sciences.
OpenML - Heidi Seibold
An online platform (openml.org) for open and collaborative machine learning
Resources for Open Science in Astronomy (ROSA) - Rachael Ainsworth
ROSA aims to compile and tailor open science best practices from around the web into a kit for astronomers to work openly from proposal to publication. ROSA will be written for use by all research levels but its mission is to supply a single resource to senior researchers to best equip them to encourage early career scientists to practice open access/data/source - in order to successfully mentor the next generation of open science practitioners we also need to target those who advise them.
Scientific computing for the terabyte-less - Timothée Poisot
In short, we need an introduction lesson in scientific computing for people that do not need a cluster, do not need big data, and do not need to have super efficient distributed code. We need robust scientific computing for the masses, and the current training does not address this. I would like to develop this resource, by publishing a series of reproducible Jupyter notebooks highlighting the best practices.
AcademicGlassCeiling - Kelly Clancy & Raquel Martins
The female (cis/female-identifying/gender non-conforming) population is grossly underrepresented among the upper echelons of academia. This platform will be a space to share their experiences and build safer, more inclusive campuses for academics and students alike. We envision users will use this platform to share workplace reviews across categories ranging from compensation to parenting support to mentorship. We hope to help users to develop robust mentoring and support networks, and empower them with the information they need to break through the glass ceiling.
Liberate Science - Chris Hartgerink
With Liberate Science, I aim to contribute to freedom and innovation in the scholarly/scientific knowledge consumption realm (long term). In the short-term, I aim to actively open up literature that remains closed despite expired copyright (‘retrospective Open Access’) instead of just focusing on how people publish new works (‘prospective Open Acces’).
Open Derby - James Robinson
In Open Derby, a small group of graduates and post-docs collaborate to analyze open data with R, Git and R-markdown, and write a manuscript for submission to an open-access academic journal. The project promotes uptake of open science by teaching open science tools on-the-fly, providing a framework for other research groups to follow, and producing a fully-reproducible academic paper.
Why not Open Science? Listening as a means to guide action - Daniela Saderi & Amie Fairs
We will develop a survey to explore the underlying reasons for failure to adopt open-science (OS) practices in academia. The survey will seek to: 1) Understand researchers’ knowledge of and engagement with OS practices; 2) Learn about obstacles that prevent them from engaging in OS practices; 3) Ask what would incentivize them to adopt OS practices. First we will test the survey in our home institutions, but our goal is to distribute the survey to other academic institutions across the globe.
Colper Science - Spile - Kambiz Chizari
We are developing a novel open access publishing system, free for the authors and the users, with the goal of accelerating the progress in science. This system provides an interactive platform for an open/collaborative peer reviewing in order to improve the quality and reproducibility of published data, and to facilitate scientific exchange between researchers. We believe Colper Science can advance the present publishing system towards a more efficient and open system.
DIY science network - Lucy Patterson
Building a network of grassroots community-led, often volunteer-run citizen science/DIY science projects. The idea is to map and network our diverse communities, support each other through collaboration, sharing of tips, experience and information about funding opportunities, to help build a bridge towards funding organisations and policy-makers, and to support constructive collaboration with different partners.
Embryo Developmental Atlas - Paul Villoutreix
Develop an interactive web based interface for the visualization of multimodal and multichannel data-driven visualizations of early embryogenesis in model embryogenesis. We rely on a data fusion algorithm that we have developed to generate integrative representations from heterogeneous datasets.
This seminar course is aimed at graduate students who have completed introductory classes in statistics and programming and are thinking about data analyses for their thesis projects. The goal is for students to develop technical skills (e.g. literate programming, version control), while also reproducing statistical analyses from the literature to gain first-hand experience with the data analysis workflow for scientific research.
ResBaz - Julian Pistorius
The Research Bazaar is a worldwide festival promoting the digital literacy emerging at the center of modern research.
Includes weekly events - Hacky Hour, PhTea, Shut Up & Write, Software Carpentry-style workshops, and community building.
We are the second ResBaz chapter in the USA.
I have built prototype software that allows one to visualize research and networks of expertise based on researcher interests and research collaborations. I have secured a partnership with the Montana State University (MSU) - Center For Biofilm Engineering (CBE) to describe Bioscience data for the next stage of the project. This work applies a novel methodology for describing researcher’s networks and areas of expertise through the application of linked open data (LOD).
The Method: a podcast- April Clyburne-Sherin
A peer-reviewed, open source podcast about the state of science
The Open Neuroimaging Masters - Grant R. Vousden-Dishington
Inspired by The Open Data Science Masters project (datasciencemasters.org) by Clare Corthell, the goal is to assemble a syllabus of predominantly digital resources available to anyone who wants to learn how to do neuroimaging. To succeed, the project will need to create a webpage with enough links to free and low-cost materials in neuroscience and data-analysis to enable everyone with an undergraduate degree, regardless of field, to make progress toward understanding principles of neuroimaging.