Projects & Participants

Andrew West (CC BY-NC-SA 2.0)

Participants join this program with a project that they either are already working on or want to develop during this program.

For the first round of the Open Life Science program, we are happy to have 29 participants with 20 projects.

Projects

Open Science Community Barcelona (OSCBa)

By: Elisenda Bonet-Carne

Mentored by: Harry Smith

This project aims to create a community of local scientists to share and promote open science in Barcelona, Spain. I would like to use as an example the OSCU and other initiatives like openscience beers in Montreal. The initial goal would be to reach researchers from different institutions: UB, UPC, UPF, UOC, UAB, etc. and meet informally in a bar/pub periodically.
During the meetings we would present/talk about what we do, we will promote knowledge exchange and will discuss on how we could improve our research in terms of open science, for example performing more transparent research and sharing data/code. Later on, the plan is to use this community to create workshops and symposia about open science and to agree on some common needs. For example, a common need in life science research group would be to have resources to help researchers in terms of data sharing or interactive paper publication. If we can define common needs we will be able to apply for some funding to cover them.
We will also use this plantform to motivate colleages from other parts of the country to create their own local community and then connect for some events.

By: Deborah Akuoko

Mentored by: Vicky Nembaware

Most sub Saharan African countries barely have quality health data for national policy making, especially on cancer. Thus, more work might be needed to improve the data quality, especially from regions with insufficient health data registries. This project seeks to investigate feasible solutions to help create a system that creates, collects and processes data efficiently for impactful research especially for driving health research and driving health related policies.
In this project, I will focus on: improving quality of gender data generated in sub Saharan Africa for research and driving health policies, creating room to make health surveillance possible and easy for policy makers to take data driven decisions, and helping establish framework to run health data registries in more regions within sub-Saharan Africa.

Infusing a culture of open science within the community of researchers at the Zuckerman Institute

By: Chiara Bertipaglia

Mentored by: Mateusz Kuzak

The community of Columbia University’s Zuckerman Institute is composed of neuroscientists at all career stages (graduate students, postdocs, faculty members). The Office of Scientific Programs, where I work, was established to build and nurture the community by fostering a professional environment that is welcoming, safer, diverse and inclusive. In its first year of life, the Office has identified relevant issues that seeks to pursue in order to support a collaborative climate of interdisciplinary research and discovery. Transparency is a key value of the Zuckerman Institute’s mission, and the Open Life Science mentor program is the perfect platform for me as the Assistant Director of Scientific Programs, to elaborate a strategy that will infuse open science best practices in the community. I hope that with the help of the cohort and the mentor, I can design a strategy to infuse a culture of open science within the community of researchers at the Zuckerman Institute. Ideally this would include power mapping, stakeholder mapping, action plans, and outreach. In the long run, work done in this project aims at developing community engagement for policy development, and will ultimately pave the way to establish the Zuckerman Institute as a golden standard for open science.

Bioinformatics Hub of Kenya (BHK)

By: Festus Nyasimi, Margaret Wanjiku, David Kiragu Mwaura, Michael Kofia Landi

Mentored by: Toby Hodges

The Bioinformatics Hub of Kenya is an entity that develops and manages training in bioinformatics and computational biology and provides a space in which research in bioinformatics is practiced.
The aim of the hub is to provide a vibrant environment that fosters research excellence, facilitating the immersive engagement of established and upcoming bioinformaticians with computational and data intensive activities in biology and the life sciences, and promoting the discipline of bioinformatics in Kenya.
Our mission is to bridge the gap between well established and aspiring bioinformaticians through peer training and mentorship to provide a pool of qualified bioinformaticians who will focus on innovation and bringing novelty to assigned projects promising quality, integrity, reliability and trust in their services.

Expanding plenoptic Python Package

By: Billy (William) Broderick

Mentored by: Rodrigo Oliveira Campos

plenoptic is a Python package for computational vision with two main components: standard differentiable models of the visual system and synthesis methods. The models operate on images and make predictions about perception or neural activity, and are relatively simple, with a small number of parameters; they can thus be used out-of-the-box on arbitrary images. To start, we will focus on spatial vision, so the inputs are expected to be static grayscale images. Synthesis methods are used to better understand models of this type. The most common applications of computational models are simulation (holding the parameters and input constant, while predicting the output) and learning (holding the input and output constant, while fitting the parameters). In synthesis, the output and parameters are held constant while the input is fit. This allows scientists to develop better intuition about which aspects of images their models consider relevant and which they ignore, as well as to carry out more efficient and effective model comparison and validation experiments. We will include four such methods, all of which have been described in the literature, but none of which have standard, accessible implementations that work on more than a handful of specific models.

@Diversidade em Foco

By: Bruno Eleres Soares, Naraiana Loureiro Benone

Mentored by: Renato Alves

Biodiversidade em Foco (@Biodiversity in Focus, in English) will merge a twitter account and a blog to promote science communication about Brazilian biodiversity. The project will coordinate daily posts communicating recent research findings about Brazilian biodiversity in twitter from researchers in different degrees of scientific career and thematic areas. Different researchers will administrate the twitter account during a week, time when they will provide daily posts about their area of expertise. Posts will be published in Portuguese in order to have higher national reach. Blog will present general information about the project and will summarize individual and community-level efforts, as well as semesterly reports of the project. Reports will be published in Portuguese and in English to share our experience to a broad audience and promote science communication. Reports will consider the number of tweets, participants, their experience during the account administration time, the number of followers and reach information in the twitter account and the blog.

Media Lab Nepal for Computational Biology

By: Sudarshan GC

Mentored by: Aidan Budd

Media Lab Nepal is only one community bio lab of Nepal focusing on democratization of life sciences through open science. It is an interdisciplinary team of students and experts with different backgrounds- basic science, engineering, journalism and management. It acted as a community partner for Darwin- India’s biggest evolutionary movement and innovation partner for Hult Prize Purbanchal University. The team is connecting innovations to entrepreneurship for maintaining sustainability. We are also partnering with community bio labs of our neighbouring countries like India, Bangladesh and Pakistan.
I want to initiate computational biology in Nepal to more number of enthusiasts from different fields during this program. Getting the support from mentors, like minded people and their mentoring will help for the sustainability of our project. At least if we can initiate this step and give platform to more number of students, we can benefit life sciences sector of whole country through open science initiative. I also want to make this initiative feasible and sustainable by creating incoming generating platform with computational biology.

InterMine Similarity Explorer

By: Himanshu Singh

Mentored by: Yo Yehudi

InterMine is a powerful open source data warehouse system. It allows users to integrate diverse data sources with a minimum of effort, providing powerful web-services and an elegant web-application with minimal configuration. But InterMine warehouses are fragmented as there’re 30 InterMines which are not interconnected. Project BlueGenes aims to integrate all the sources and provide a single interface to access the data of all 30 InterMines.
This project aims to develop a javascript based tool which will be embedded on BlueGenes list pages (which can be of genes or proteins). This tool will allow users to find similarities between different genes or proteins that are provided in the list. In order to enable this, we’ll make an explorable graph visualization of the relationships between InterMine entities (proteins or genes). Each entity or object will be represented as a node.
The idea is that visualizing things helps us to spot patterns. So, we’ll have this tool, which will visualize the interactions and similarities between different entities and there will be options to tweak the appearance/structure to make things more explorable.

Open Connect Platform in Africa

By: Lilian Juma

Mentored by: Caleb Kibet

In Open community, there is disconnect between Open practitioners and advocates hence need for platform to connect everyone within open landscape. Therefore, Open Connect will be a platform where everyone across the divide will be part of the solution through lessons, trainings and mentorship. This is an interactive platform targeting students, early career researchers, policy makers and senior researchers in shaping Open policies each country at a time in Africa. Since Africa poses different and unique development dynamics, development of all phases of this project will put into consideration various divides such as rich vs poor, rural vs urban, research literate vs research illiterate among others.

EMBL Bio-IT Community Project

By: Renato Alves

Mentored by: Malvika Sharan

Bio-IT project at the European Molecular Biology Laboratory (EMBL) is an initiative established in 2010 to support the development and technical capacity of its diverse bio-computational community.
After finishing my PhD recently at EMBL, I took the next role as a Bio-IT community coordinator within the same organisation. In order to perform effectively in my job, I want to formally gain community management skills and understand the various tasks and responsibilities within the Bio-IT project. With my application to the Open Life Science program, I want to be paired with a mentor, potentially Malvika Sharan, who is my predecessor in Bio-IT. I want to take this opportunity to ensure a smooth knowledge transfer within the management team of the Bio-IT project and navigate my own path and future prospects as a community manager.

Oxford Neuroscience Open Science Co-ordinator: Changing Culture

By: Cassandra Gould van Praag

Mentored by: Naomi Penfold

The Wellcome Centre for Integrative Neuroscience (WIN) and other centres in Oxford Neuroscience recently received large awards which include substantial components of open science. These centres have thus far focused on developing the infrastructure required to share data and tools, and are now ready to turn their attention to the ethical, ecological and social challenges of supporting the uptake of open science practices. I have been recruited as an Open Science Co-ordinator for Oxford Neuroscience, to work between departments and alongside partners in other institutions to develop policies and recommendations for good governance that work for individual facilities (e.g. WIN), across departmental boundaries within medical sciences (e.g. Oxford Neuroscience), and then beyond into the wider University and national networks. The aim is to develop an open science community through an understanding of the principles of behavior change, including recognizing scientific and individual risks and benefits for research participants, researchers (at all levels), and the institution.

AMRITA: an online database for herbal medicine

By: Anunya Opasawatchai, David Chentanaman

Mentored by: Holger Dinkel

In South East Asia, herbal medicine has been used over the century as preventive and therapeutics intervention. However, due to the scarcity of scientific evidence, the use of herbal medicines is limited to local wisdom. Several constraints such as the absence of funding, patent issues, and most importantly, the lack of modern scientific approaches have prevented the pathway to this gold mine of drug discovery. Here, we propose the development of AMRITA, an online web-based library of medicinal herbs that include their phylogeny, medicinal properties, known active components and related scientific literatures that is open publicly to the research community world-wide. This platform would facilitate the collaboration of researchers across the fields of biological, pharmaceutical, and clinical sciences in establishing a solid foundation of medicinal plants and enabling the use of these plants in modern medicine.

How to build an healthy and open lab

By: Elsa Loissel

Mentored by: Daniela Saderi with Patricia

I would like to create a one-stop shop for new life science PIs who want to start their labs using principles, resources and practices found in the open space, but who may struggle to find and access this content themselves. More importantly, I would like to design an efficient communication strategy to bring this relevant content to young PIs in a way that saves them time and energy. This would first require understanding what PIs most needed when they started (and therefore which already existing resources are actually useful), and how it should be delivered to them - in which form, through which channels (e.g. young PIs newsletter), at what time(s). Then, I would like to curate existing content, repackage it in an easily accessible and “digestable” form, add to it, but also create readily usable tools (e.g. templates - not just things people have to read). Topics would include how to work openly and inclusively (e.g. lab codes of conduct, lab manuals, leading inclusive meetings, setting up a healthy lab culture etc.); how to do research open (preprints, toolkits with software to work open, project management tools etc.); how to train the next generation of open scientists; and how to open your work to the public. Finally, I would like to approach organisations and institutions to help more young PIs get access to these resources.

Benchmarking environment for bioinformatics tools

By: Zoe Chervontseva

Mentored by: Luis Pedro Coelho

The aim of this project is to provide a flexible protocol and unified instruments for iterative benchmarking of bioinformatics tools solving various problems. The results of benchmarking for each particular task are to be published as a blog post. The posts are to be automatically updated each time somebody provide new data on the performance of any considered tool. There should be an ability to add new tools as well as new datasets to an existing comparison.

EDAM ontology

By: Matúš Kalaš

Mentored by: Björn Grüning

EDAM ontology is a long-established project, defining a common, controlled vocabulary in the form of a network of concepts and terms. EDAM covers topics, operations, types of data, and data formats used in computational life science, i.e. in analysis of biological data, with some bias towards molecular life science and cellular bioimaging. Bioimage informatics was the first larger extension of EDAM beyond mainstream bioinformatics and computational biology, with highly successful development model engaging a broad community of bioimaging and bioimage analysis experts. The EDAM-bioimaging work was initiated by Jon Ison, Josh Moore, and others, and I have been responsible for its further coordination.
EDAM is used in applications such as registries of computational tools or training materials (contributing to open science), in the Common Workflow Language (CWL), or in automated workflow composition. It is also in the process of implementation in various parts of the Galaxy project. EDAM is developed in a transparent and participatory manner, similar to modern open source software (it is available under CC BY-SA).
The goal of this concrete mentorship project is to further extend EDAM, so that other communities can benefit from it, and from the applications and use cases it fosters.

Improving Documentation for Open Data and Software in the Agricultural Research Community

By: Kristina Riemer, David LeBauer, Emily Cain, Jorge Barrios

Mentored by: Katrin Leinweber

We are members of the Data Infrastructure for Agriculture Group at The University of Arizona. Our mission is to provide scientists with open software, data, and computing that improves development of productive and sustainable agricultural systems. One of our persistent hurdles has been enabling and motivating the community to use our software and data.
To address this, our project will focus on improving documentation for data and software that our group develops, as well as identifying and sharing best practices with the broader community. We will include the TERRA REF project, which produces high-resolution sensor data on crop plants, and the drone pipeline, which automates steps in the use of drones to study crops. Both projects produce open data (CC0 and CC-BY) and software (MIT/BSD compatible).
Our goal is to make our products more usable for our intended audience, which is primarily scientists across a range of disciplines from computer science to remote sensing. We plan to have each person in the group complete a sub-project that can be finished in 15 weeks. Each sub-project would result in an accompanying blog post describing the best practices implemented.

Improving open platform accessibility

By: Christine Rogers

Mentored by: Hao Ye

I’m a member of the technical team for LORIS (github.com/aces/loris), an open-source neuroinformatics platform that allows researchers to collaboratively collect, curate and share data on the brain, behaviour and genes.
Aside from Jupyter notebooks, gitlab, and a few platforms that focus on data storage and linear processing paths, it can be hard to find platforms where researchers can safely collaborate with real transparency, while sharing as they go through a data collection lifecycle the actual workflows of their open science practices. I work already with an open-source project that provides these tools, but our platform can be challenging to adopt for new projects without dedicated technical resources, given the depth of knowledge and time required.
My objective for this project is to begin tackling this from a few angles, including documentation, publication, and nudges in our code development process. I believe it is feasible in this timeline to also pilot open tools with a new project or as an extension to an existing project – to start putting this idea into action. What problem(s)

Enabling open science practices in biology education

By: Sandy Kawano

Mentored by: Fotis Psomopoulos

The proposed project would establish a foundation for developing a tutorial on training researchers in biology to adopt more open science practices. The main goal would be to design a website (e.g., through GitHub) that would contain different chapters on how to accomplish different open science achievements (e.g., designing a Code of Conduct for collaboration, developing a data management plan, setting up an Open Lab Notebook) and that could be easily cloned to their personal websites and modified for their specific purposes. As an extension, I am hoping that this could then be expanded into a university course for undergraduate and/or graduate students or even as a workshop that could be help at different education centers, museums, or conferences. Not only would this allow junior faculty to get on the right foot of developing an open and inclusive lab, it would also help train the next generation of open scientists who trained under the faculty member. By making these resources freely available, it would also help maintain open lines of communication between lab members and make sure that expectations of the faculty mentor and student / staff mentees are fully transparent so that the mentoring process can be improved for science mentees.

Open Science UMontreal (OSUM)

By: Samuel Guay, Danny Colin

Mentored by: Andrew Stewart

In 2019, we founded Open Science UMontreal (OSUM) because we believe in an Open by Design approach when it comes to Science. As a student initiative, we want to establish an inclusive and collaborative community where students and researchers at all stages of their careers feel welcome to learn, share, and discuss open science values, principles, and practices. By raising awareness of current issues, we hope this project will instigate a culture shift and help people realize how they can immediately benefit from using open and reproducible practices. As open science is a broad and wide-ranging concept with domain-specific definitions, we want to provide opportunities to meet and encourage the exchange of ideas within and across fields because we can all learn from each other. Throughout the Open Life Science mentorship program, we will focus on laying the foundations of our initiative by developing our web platform and organizing some-on campus activities.
Ultimately, we aim to facilitate networking between local “open initiatives” through Open Science Canada. Inspired by the Australia and New Zealand Open Research Network and the Open Science Communities in Europe, we hope that Open Science Canada will draw together like-minded people across the country and foster collaborations and the sharing of open resources and knowledge.
If you’re reading this and you’re interested in open research feel free to come chat with us on chat.openscience.ca, an open-source alternative to Slack! We want to get to know you (and your initiative)!

Creating network of Data Champions at the library of Free University of Amsterdam

By: Lena Karvovskaya

Mentored by: Patricia

From February 1st I am starting a new position as community manager RDM at the library of Free University of Amsterdam (VU). My ultimate goal is to bridge the gap between researchers and support personal by creating opportunities for networking and collaboration. The project that I would like to develop as part of the Innovation Leaders programme is setting up a network of Data Champions. Data Champions are local community member willing to share their discipline-specific expertise with colleagues; they advocate good RDM practice and advise and proper handling of research data.
Similar programs have been launched at the University of Cambridge, TU Delft, and Wageningen University. The main goal of the Data Champion programme is to drive cultural change towards open science and open data.

Participants

The GitHub avatar of

Chiara Bertipaglia

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@ChiaBertipaglia

Columbia University’s Zuckerman Institute , USA

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Festus Nyasimi

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@Festus_nyasimi

International Centre of Insect Physiology and Ecology (ICIPE) , Kenya

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David Kiragu Mwaura

@MwauraKiragu

Institute of Primate Research , Kenya

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Kristina Riemer

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@KristinaRiemer

University of Arizona , USA

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Michael Kofia Landi

@CofiaLandy

International Livestock Research Institute , Kenya

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Lena Karvovskaya

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@LangData

Free University of Amsterdam , Netherlands

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Lilian Juma

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Information Training and Outreach Centre for Africa , Kenya

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Emily Cain

@magic_milly

University of Arizona , USA

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Margaret Wanjiku

@meg_wanjiku

International Livestock Research Institute , Kenya

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Sandy Kawano

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@MorphoFun

The George Washington University , USA

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Naraiana Loureiro Benone

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@nlbenone

Museu Paraense Emílio Goeldi , Brazil

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Samuel Guay

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@SamGuay_

Université de Montréal , Canada

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Jorge Barrios


University of Arizona , USA

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Anunya Opasawatchai

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@pk_suta

Mahidol University , Thailand

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Billy (William) Broderick

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@wfbroderick

New York University , USA

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Elisenda Bonet-Carne

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@bonetcarne

BCNatal Fetal Medicine Research Center , Spain

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Bruno Eleres Soares

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@Bruno_E_Soares

Universidade Federal do Rio de Janeiro , Brazil

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Cassandra Gould van Praag

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@cassgvp

University of Oxford , UK

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Christine Rogers

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@xtinerogers

Montreal Neurological Institute, McGill University , Canada

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Danny Colin

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@dannycolincom

Université de Montréal , Canada

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David Chentanaman

@davidchenn

Osaka University , Japan

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David LeBauer

@dlebauer

University of Arizona , USA

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Elsa Loissel

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@elsasci

eLife , UK

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Deborah Akuoko

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@eminka_da

University of Manchester , UK

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Zoe Chervontseva

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IITP RAS , Russia

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Himanshu Singh

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@lazycipher

Galgotias University , India

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Matúš Kalaš

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@matuskalas

University of Bergen , Norway

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Sudarshan GC

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@Sudarsh07847591

Media Lab Nepal , Nepal

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Renato Alves

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@renato_alvs

European Molecular Biology Laboratory (EMBL) , Germany

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