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.
Mentored by: Juyeon Kim
Keywords: Open Science, Education, Outreach, Meta-research, Big Data, Data Science, Bibliometrics
This project aims to create a template for an engaging Open Science course tailored to the needs and abilities of high school students. It will use a catchy premise of learning Data Science to introduce students to good (open) scientific practices and explain the importance of such practices. The teaching materials will be composed of several modules, each including short presentation on key topics, reading, quizzes, and hands-on activities, and a mini-project. For the latter, we will apply Data Science techniques to investigate science itself, specifically a corpus of scientific literature (Big Data, accessed via free Dimensions accounts). Students will plan and conduct meta-science projects on chosen topics. In other exercises, students will track the life cycle of a scientific publication and get into the shoes of one of the researchers. We will explore some of the fundamental issues that modern science and scientists face, including incentives, fraud, questionable research practices and biases, and how science intersects with the broader society and policy. Overall, this course will deepen students understanding of science as a collective activity and a complex system with many players - helping young people to navigate their career in research and develop critical skills for other career paths.
By: Dario Basset
Mentored by: Alessandra Candian
The project consists of finding the right ways (media, news and tools) to spread open science concept and find adepts
I want to create a platform to publish scientific articles from all science disciplines that would allow: - Open peer review – by sharing reviews with names of reviewers, we ensure a more fair reviewing process - Open post-publication review – allow for people to comment on articles to share their view, experience reproducing results, etc. - Free publication - Random assignation of reviewers to articles – ensures fairness in the publication process, allows junior scientists to participate in the process
Mentored by: Elisee Jafsia
It was reported that “there are over 4000 x-ray machines in Nigeria with less than 5% of them under any form of regulatory control of the Nigerian Nuclear Regulatory Authority (NNRA).There is, therefore, a need for proper Quality Assurance QA testing during installation and control tests at regular intervals as this will further help to reduce repeated radiograph and rejected films thereby saving cost and reducing patient doses. This project is aimed at deterring the level of compliance of QA across radiology centres in Kano State and to also move ahead to develop a robust, multi-adaptor quality control kit for all forms of x-ray equipment. This will help to develop local capacity, improve healthcare and promote wellbeing for all ages of Nigerians in-line with Sustainable Development Goal 3.
By: Elena Giglia
Mentored by: Emma Karoune
Keywords: Scholarly communication, Open Science, FAIR data management, training
Objective: to provide a FAIR by design training course on Open Science The project aims at creating FAIRer teaching material on my subject of expertise, Open Science, improving my teaching skills by attending your course on opening up every step of the research cycle alongiside researchers in different fields.
Mentored by: Siobhan Mackenzie Hall
Keywords: ethics, neuroscience, open-research, computer models reproducibility, open source software
Working with the Alan Turing Institute I want to create a framework that allows questioning of ethical standards and reproducibility of Computer Models in Computational Neurobiology, both specifically within my PhD work, and taking this as an example for others to learn too. - My PhD project work includes working with open source software (MCell https://mcell.org/, BioNetGen https://bionetgen.org/ and Biodynamo https://biodynamo.org/) to create biological predictions of how memory works. It is therefore, both, intrinsically embedded and important that the work I create for my PhD is as accessible and collaborative as possible. - I plan to implement the Turing Way (https://the-turing-way.netlify.app/welcome), Turing Commons (https://turing-commons.netlify.app/welcome/) and Data Hazards (https://datahazards.com/) principles, as I think about ethical implications of my work. This way, I will use my PhD as a case study and share it with the wider peer community. - Explore these questions by designing seminars and workshops with people knowledgeable in different fields. E.g.,workshop where people with expertise in research of Ethics and people researching in Computational Neuroscience come together. - Offering workshops and collaboration cafés where we can work through these topics with an intersectional and collaborative approach, offering different solutions to problems that arise.
By: Jennifer Ding
Mentored by: Malvika Sharan
Keywords: civic tech, data collection, urban data science, mapping
ODC (Open Data Custodians) is an open tool for connecting public domain Github repo data to a DB/API. Inspired by the BigScience Data Governance Framework, this project seeks to empower repo maintainers to do more with their data and create new pathways for responsible data sharing in the open AI ecosystem.
Mentored by: Anne Treasure
Keywords: Generation Z researchers, Research Trends, Open Community, Life Science, 2022
Generation Z stands to become the new entrants into the world of research from 2024. I believe new systems and easier ways of accessing information with more vocal communities are needed to usher in the new generation. But to do so, the new bachelor and high school students must be the recipient of effective scientific communication to help them realize the existing communities and opportunities in life science research in India. As a penultimate bioengineering student, my exposure to existing communities is recent and new. This fact allows me to understand and appreciate the importance of such communities in guiding students with a passion for research in life sciences. Life Science in 2022 India is a concept that seeks to unite parallel enterprises by individuals across the nation under one banner. The goal is to provide a complete and interconnected picture of Life Science research and communities in India. Simultaneously, as a founder of a Bioengineering Chapter in my institution, I will be applying our findings to build and train my colleagues and juniors to have the tools and awareness to choose their next steps in research. Finally, we measure the success of this project through the successful publication of a paper that encompasses the findings and suggestions for building a better and more robust open community of life science research in India.
Mentored by: Mayya Sundukova
Keywords: Mental health, researchers, Tools and techniques, open resource
Mental health among researchers is a huge neglected burden that has significant impact on their lives and the people around them. Majority of the focus on mental health is in capacity building for mental health research or offering sustainable mental healthcare. The lack of conversations around how students undertaking research fail to complete projects or progress beyond certain levels in research shines a bright light on the intensity of neglect on the mental health of researchers. It is therefore paramount to create awareness and avail tools catered to researchers needs. The project focus is to develop an open online support resource for primary mental health catered to researchers particularly scientific researchers. This platform will contain educational materials concerning emotional health which sits at the core of mental health. It will also contain self-assessment tools and techniques for developing mental resilience. In addition to that, the resource will contain a peer support network that will offer help and emotional support. The overall objective is to avail help, progress monitoring and increased understanding of the importance of mental health wellbeing among researchers.
Keywords: Mapping, Visualisation
This project is about creating an interactive map that locates all the past and present mentors, mentees, experts, and speakers who participated in the Open Life Science (OLS) programme. The map will be created using the Shiny R package. It will help provide the geographical reach of the programme. The aim will be to create a map that automatically updates whenever new information in stored in the database. It will also have an option to display only the mentors/only the mentees/only the experts/only the speakers. If time permits, the project will be further expanded to visually summarise other information like a table with area of expertise of the mentors, experts, and speakers.
By: Marie Nugent
Keywords: community building, crowdsourcing, collective intelligence, engagement, participatory research, genomics medicine, bioinformatics, healthcare, data science, population genetics, diversity, equity, health outcomes
The Diverse Data initiative at Genomics England intends to build community spaces to: Facilitate effective engagement; enable creates crowdsourcing of tools and collaborative opportunities, and; build relationships and understanding across communities around the complex nature of diverse data for genomic medicine. These communities will involve a range of researchers, clinicians and healthcare professionals, patients, publics and cultural partners.
Mentored by: Sara Villa
Keywords: community, introductory course, early career researchers, practitioners, Ireland
Under Agape, would like to build a community of open science practice to grow our work up to date in a way that can catalyse changes in researchers’ perceptions of open science across Ireland and later internationally. The first step we underwent was creating a massive online open course (MOOC) by early career researchers (ECRs) for ECRs and other academics. The content of the MOOC is currently under review and is planned to launch in the late summer. We hope to grow the learning experience further by hosting workshops and events where individuals can learn from experts and share their own experiences about open science practices.
By: Hari Sood
Mentored by: Nadine Spychala
Keywords: education, pedagogy, social justice, online learning
Over 2020/21 I was working on launching a social justice learning platform called Pyxium: https://app.pyxium.co/. It became apparent after working on it for a while that this should exist as an open, free and community driven platform, rather than a private for-profit enterprise. The codebase is currently private, written exclusively by me. There is a lot of work that needs to be done to prepare it for open sourcing - I see it as fitting into a few different categories: * Technical: Commenting throughout the code, cleaning the code up, clarifying folder/file structure, rewriting confusing functions/variables, ensuring basic security * Collaboration: Documentation, contributing guidelines, code of conduct, role distribution * Governance: Strategy, project management, community roles, contribution process and requirements * Community: Engaging developers (and educators, SJ advocates, designers…) with the project And probably much more!
Mentored by: Caleb Kibet
Keywords: Open science, Community, Nigeria
Inspired by the Open Science (OS) movement that focuses on making science more open, improves the quality, accessibility, and efficiency of science and education, Open Science Community Nigeria (OSCN) was established to provide a space that will encourage and promote openness, transparency and reproducibility in science among scientists, network of researchers and societal stakeholders in Nigeria. There are quite a number of some initiatives in Nigeria such as AI Hub, Nigeria, Python Nigeria and R User groups that mainly promote data science and computational sciences. However, none there exist a single community that instilled responsible conduct of research, promote the principles of open science and or establish a guiding principles and core values or policies that support scientists, researchers, and societal stakeholders to meet, inspire and co-create important things together as a community. Thus, we aim to establish and develop an open science community in Nigeria where newcomers and experienced peers interact, inspire each other to adopt Open Science practices and values, identify opportunities and pitfalls, and provide feedback on policies, infrastructure, and support services as does in other regions of the World. We aim to specifically target scientists, researchers and students who are passionate about open science but have little to no experience with open science principles and practices.
Mentored by: Kim Martin
Keywords: Ontology, RSE (Research software engineer), Semantic technology, Data science, Artificial Intelligence (AI), Knowledge engineering
Our project aims to map the relationship between people, skills and technologies, structured under the AI and data-science landscape, in order to develop an ontology that can assist Research Software Engineers (RSE’s) to better manage their teams and affiliates. It also aims to enable better collaboration within the RSE community and between research institutions. This project is driven by the growing need for RSE’s by researchers, as research is becoming increasingly reliant on data-driven technologies, and within the academic community itself, there is an emphasis on providing reusable, reproducible data which is not a skill that most researchers have. By creating a semantic overview of the interaction between skills, technologies and the key role-players in the RSE community, this ontology will be able to provide information on the research fields that each RSE has background knowledge in, their development skills, and the services that they are willing to provide clients, enabling a way in which suitable RSEs can be assigned to projects where they will be able to provide software development and software-development-related assistance. This project also aligns with the thinking supported by Open Science, as the ontology is aimed to be reusable and reproducible.
Keywords: Research landscape, RSSE, RSE, community
This project aims to identify African research groups that are heavily involved in in-house research software development and could potentially benefit from being part of RSSE-Africa and the larger global RSE movement. This may, for example, include data science research initiatives at universities, bioinformatics or astronomy groups, computational social sciences and digital humanities groups, and many more. Furthermore, the project will identify open communities of practice related to research software and systems engineering, such as RLadies, Python User Groups, and HPC User Groups that could potentially supplement the support RSSE-Africa is providing. For communities of practice, we will collect information on several attributes, including their focus area, communication platforms, activities offered, and more. This information will be shared in a Google Spreadsheet on the RSSE-Africa website and will be open for the community to contribute to and update as necessary. The RSSE-Africa website will simultaneously be updated to improve content and navigation. The project will build on work done by members of the RSSE-Africa community and the Research Software Alliance (ReSA).
Mentored by: Lena Karvovskaya
Keywords: community building, training, health reseach, artificial intelligence, collaboration, reproducibility, reprohacks
The AI for Multiple Long-term Conditions (AIM) research programme consists of seven consortia, all working with artificial intelligence methods to understand multiple long-term medical conditions. The Research Support Facility (AIM RSF) is a collaboration aimed at supporting those consortia. Our project aims to foster a community formed from the AIM RSF and seven AIM consortia and support collaboration from three core approaches: - supporting the upskilling of researchers so that their work may meet the highest ethical, technical, and reproducibility standards - ensuring that existing technical and domain expertise is well-documented and understandable to a wide audience - leading by example and empowering community members to champion open and collaborative research practices. We propose to do this through hosting workshops and events centred around collaborative work. We will start by collating and contributing to training materials around open science and reproducibility and supplement with workshops on tools that support openness, collaboration, and reproducibility. We aim to host regular “Collaborations Cafe” sessions, where community members exchange knowledge, propose projects, and get feedback. Ideally, our project would culminate in a ReproHack, where teams check the computational reproducibility of research, provide feedback, and further develop their technical skillset.
Mentored by: Sara El-Gebali
Keywords: Bioimaging, super-resolution, open hardware, open microscopy, image analysis
Super-resolution microscopy (SRM) bypasses the diffraction limit and makes the nanoscale visualization of subcellular structures and dynamics possible. Yet the complexity and high expense of SRM setups often obstruct access to the sub-diffraction information for biologists. As a team working at the interface of optics and cell biology, we are motivated to build up an online platform that documents our homemade, powerful, and cost-efficient super-resolution imaging systems and analytical tools that are currently running and under development in our group, as well as to contribute to the expanding global community of open science. The proposed platform will provide adequate information for researchers in need of reproducible SRM. It can benefit cell biologists who are interested in advancing their research with the assistance of super-resolution imaging techniques, such as single-molecule localization microscopy (SMLM) and super-resolution optical fluctuation microscopy (SOFI) that our team focuses on, but lack the experience in selecting optical components, constructing light microscopes and processing the data acquired. We plan to build the platform around three main topics: SRM open hardware (including the open control software), image analysis tools, and an educational core around optics.
Mentored by: Yo Yehudi
Keywords: Open Science, Implementation hurdles, Hackathon, Life Science
OpSciHack is an open science-focused hackathon that we, Open innovation in life sciences - OILS would like to organize as an annual event. The hackathon aims to solve problems in open science and open science problems. In each iteration of the hackathon, we would like to focus on one pillar of open science (OS) and develop solutions to encourage a culture of OS in research communities. At the hackathon, participants can either come up with their own problem statements or chose one to work on from our list. The questions will focus on: (1) difficulties that prevent them from fully implementing and practicing some or all aspects of OS in their science networks/ institutions/universities, and (2) problems that can be solved through OS. OILS will provide support to the participants by tapping into the OS network in Switzerland and introducing them to necessary experts and tools. An example of such a problem could be the absence of a searchable data repository in their university that contains links to all published datasets from the participating research groups - such an infrastructure would encourage the generation and sharing of well-annotated data. At the end of the event, ideally, the participants would have actionable steps and solutions that either can be directly implemented by them or proposed to competent authorities. Starting out at the swiss national level, we hope to grow OpSciHack involving global participation.
Mentored by: Stephane Wapouo Fadanka
The Hub portal and academy seeks to create a curriculum and a data portal targeting young researchers and incoming biology students to be equipped with data management skills, project planning skills and basic bioinformatics skills. Pauline Karega has already kickstarted the hub portal where we hope to gather bioinformatics interested undergraduates and connect them to a platform where they can interact and get connected to opportunities which will be automatically gathered from sources such as twitter using keywords and integrated to the backend of the hub portal at BHKi. Initial value proposition will be create an academy that gives basic scientific research training and skills to these students who will be embarking on their research projects in the final year of study; we hope to equip them with basic programming skills that will help in analysing biological data and guide them through designing and planning a research project. Eventually we hope to evaluate the uptake of knowledge through hackathons and collaborate with high ranking institutions for our mentees.
Keywords: Online platform, compendium, didactic schemes, didactic figures, multidiscipline
The idea is to create an online platform that hosts any sort of didactic material. It can be a site that gather in an organized way different educational materials to be used by university professor or schoolteachers with their students. At first it can be a link aggregator from materials dug from internet, but in a long term the site will be open to researchers to upload their material editable enough that others can translate to their own language. This material will be accessible so different professionals can download it and they will be encouraged to rate and comment about the material used. To accomplish this, the idea needs at least two moderators to approve the material uploaded, an curator to organize the site, and a digger to find links and people that wants to upload their material.
By: Alden Conner
Mentored by: Mallory Freeberg
Keywords: polar science, sea ice, conservation, climate change, environmental science, product management, product roadmap, stakeholder map
As part of a NERC proposal that would fund three years of further work on the IceNet project, I have proposed a work package called “Demonstrating and deploying real-world solutions”, with the first part of that work package consisting of stakeholder engagement leading to creation of product roadmaps for both the IceNet forecast and the supporting digital infrastructure. I would like to outline a plan for performing this stakeholder engagement openly via the GitHub repository, leading to collaboratively-generated user requirements for the final products. I will consider how to reach stakeholders and engage them in open discussion on GitHub, and how to organise that work to generate a mutually agreed-upon set of user requirements. Stakeholders will include scientists such as polar researchers and AI researchers, who will contribute to requirements for the forecasting capabilities, as well as additional end-users such as conservation researchers and indigenous communities, who will help shape software requirements.
By: Nicky Nicolson
Keywords: biodiversity informatics, species description, specimen citation, research management, record linkage, document production
This project is developing a prototype “extensible notebook for open specimens”. This is a link-aware editor for semi-structured data based on personal knowledge management software (Obsidian). This environment plus standard open science tools (reference management tooling and pandoc document production) could help the adoption of open science principles amongst biodiversity researchers. The project is split into three main areas of investigation (effort so far has been focussed on the first): 1. Working environment: can we extend personal knowlege management software to reference biodiversity-relevant data classes (in a similar way to how bibliographic citations are managed) - We have developed a set of Obsidian plugins which facilitate easy access to the data resources needed to (a) work with existing species descriptions from literature and (b) recognise and formally describe new species. (Entry for the forthcoming Ebbe Neilsen challenge) 1. Review environment: can we generate snapshots for peer-review /publication 2. Publication environment: can we package data for harvesting into data aggregators We aim to enable researchers to develop the “digital extended specimen”, but without being prescriptive about their workflow: open to access and publish the necessary data - but also open to choose how to organise their work.
By: Rushda Patel
Mentored by: Hans-Rudolf Hotz
Keywords: ethics, neuroscience, open-research, computer models reproducibility, open source software
Cardiovascular diseases are the leading cause of death around the world and account for nearly 32% (2019) of all global deaths. The advancement in omics technologies over the recent years has provided a deeper understanding of the molecular processes and dynamic interactions involved in diseases which have helped in identifying various diagnostic, and prognostic biomarkers along with therapeutic targets. In my project, I aim to build a tool to carry out multi-omics analysis and profiling encompassing major CVD diseases using data from relevant datasets. The biological interests of this tool would be the identification of differentially expressed genes, proteins, metabolites, and transcripts, progression-associated genes, SNPs, pathways and networks involved, survival analysis, and small molecule identification. It would also include a user-friendly repository of data from research articles which would be easy to navigate This tool would be a one-stop solution platform for CVD multi-omics that would help researchers in drug discovery, unveil disease mechanisms, identify biomarkers,
By: Aman Goel
Mentored by: Mariana Meireles
Keywords: research software engineering, open science, open education, community
The Undergraduate’s Guide To Research Software Engineering aims to provide an open-source, dynamic, and accessible collection of resources on Research Software Engineering to undergraduates and newcomers interested in knowing more about the field. The project aims to develop resources majorly around the following four areas: 1. Information and Background of Research Software Engineering * This area would cover all the necessary context, history, background information, and the current situation of the Research Software Engineering movement across the world. 2. Training and Education Resources * This area would cover all the necessary resources and materials to help develop skills required by a Research Software Engineer. * It would cover existing resources as well as could be expanded to include new material. 3. Job Board for Entry Level Positions * This area would primarily provide entry-level job listings in the field of Research Software Engineering and Open Science to lower the entry barrier for newcomers. 4. Support and Community Engagement Resources * This area would provide support to newcomers in the form of open access community platforms as well as aim to provide help from experts on a case-to-case basis.
By: Mayya Sundukova
Mentored by: Natalie Banner
Mentored by: Michael Landi
Keywords: Bioinformatics, Students, data analysis
Bioinformatics Secondary School Outreach (BSSO) is an initiative to develop bioinformatics capacity among High school students in Nigeria and this will create early interest in genomics data analysis among the students and equip them with the relevant skills and knowledge in Bioinformatics. Bioinformatics Hub Nigeria will be training these students on how to use Bioinformatics tools and pipelines and this can be achieved by establishing Bioinformatics research clubs in the visited schools to facilitate the trainings. We would be working alongside with other sister organizations to achieve this goal
I am a Research Application Manager at the Alan Turing Institute. I work with project teams to adapt research outputs for real-world problem solving.
I’m a recent Computer Science and Maths graduate from the University of Delhi
Anelda is the founder of Talarify, a South Africa-based consultancy working with researchers and postgraduates to help grow digital, computational, and open science literacy. She has a formal background in bioinformatics, but spend most of her time working in interdisciplinary teams these days. Main projects currently: 1) afrimapr, funded by Wellcome Open Research, where the team is working with data science communities in Africa and beyond to help make African data more accessible via the development of R building blocks; and 2) ESCALATOR - growing an inclusive and active community of practice in Digital Humanities and Computational Social Sciences in South Africa.
Umar Ahmad is currently the Head, Department of Anatomy at Bauchi State University, Nigeria. He is also a founder and CEO of BioSeq, a bioinformatics company that translates omics data into informative knowledge by providing quality high-throughput sequencing (NGS) data analysis. His work in basic and translational research is focused on developing targeted therapy for human bladder cancer, colon and lung cancers with primary focus on genomics (WGS, WES) and transcriptomics (RNA-Seq, scRNA-Seq, Microarray) data integration to investigate the regulatory pathways that drive tumour recurrence and progression. Additionally, Umar works in an international team of scholarly professionals at AfricArXiv - the pan-African Open Access portal – towards increased discoverability of African research output. His role involves facilitating manuscript submission moderation and quality assurance as well as representing AfricArXiv at international meetings, events and webinars. At the Science Communication Hub Nigeria, he supports a team that provides mentorship, implements training and community building for the next generation of Nigerian scientists. Umar is a fellow of Accelerating Science and Publication in Biology (ASAPbio), a mentee and a member in The Carpentries community and a member of Open Bioinformatics Foundation. He is also the current Regional Coordinator (North East) of the Nigerian Bioinformatics and Genomics Network (NBGN). Moreover, Umar maintains a community of scientists who are passionate about bioinformatics in a slack workspace called Bioinformatics Hub to facilitate sharing of bioinformatics knowledge in Nigeria. (Link: https://docs.google.com/document/d/14ayo1wHRpDvF-L5yHaBHyEqXW29EqEApfCtf3F3xiq4/edit?usp=sharing)
Jennifer Ding is a Research Application Manager at The Alan Turing Institute. Her research interests are in AI ethics and privacy by design
I’m a Community Manager working to facilitate collaboration within a project using AI to better understand multiple long-term conditions. During my (psycholinguistics) PhD I became fascinated with open research and got into teaching reproducibility and R.
I love Science
I am a PhD student with several interests that keeps me busy outside the lab. I dabble in science communication
My name is Ken Mugambi. Currently am a masters student at Pwani University
I work as Community Manager for the Diverse Data initiative at Genomics England and I’m interested in building an open source tooling and sharing network across a range of people developing exciting tools that enhance our understanding and application of diversity in genomics data and healthcare.
Medical engineering with a passion for neuroscience and biophysics.
I am a ready-to-learn glass half full kind of person. I am passionate about transferring knowledge. I believe that as you transfer knowledge
I am a Bioinformatics scientist who is very passionate about mental health. I am equally passionate about neuroscience and would like to explore research in that field.
First-year PhD student with research interest in the interface of optics and biology
I’m a PhD student in Federal University of Rio de Janeiro and currently I’m evaluating the impact of deforestation in multiple facets of stream fish diversity. Besides my research
I am a Statistician by training. I have completed the Google Summer of Code 2020 with the Turing team of the Julia language organisation. Recently I have written the “R Developer’s Guide” with a funding support from the R Foundation.
I want to bring love into academia