Whilst it is generally agreed that scientific research needs to be peer-reviewed as part of the publication, this stipulation doesn’t always extend to peer-reviewing code. We aim to build infrastructure that clearly lists not only journal policies with regards to code artefacts, but also compliance with journal policy.

Led by João Paulo Taylor Ienczak Zanette, Isaac Miti and Yo Yehudi

Aim

Scientific research these days often involves code as part of the research methods and/or outputs. Whilst it is generally agreed that scientific research needs to be peer-reviewed as part of the publication, this stipulation doesn’t always extend to peer-reviewing code, despite the fact that the code may be an integral part of producing the results, and indeed, bugs in the code may result in incorrect scientific results. 

We hope to revive an initiative within the Code is Science project to list popular scientific journals and their policies with regards to code openness and peer review. We aim to build infrastructure that clearly lists not only journal policies with regards to code artefacts, but also compliance with journal policy. This infrastructure would allow contributors to submit and edit entries for journals, including specific evidence with regards to policy compliance levels. Users of this database would be able to search based on specific criteria, such as code or data openness policies, code peer-review policies, and journal policy compliance level. This would be beneficial for people choosing where to submit their papers and/or which journals to review for. In addition, having information clearly available might incentivise other publishers towards open practices.

Work at the Sprint

We propose to expand the current prototype code, building a more robust backend, submission form and data schema. Whilst there wouldn’t be time to complete the entire architecture, we would be able to at least design the structure of the data, such as journal name, open-data policy, open-code policy, policy compliance, proof of compliance (or compliance issues) and so on, as well as mock-ups of what the user interface might look like based on the data design. 

We are looking for…

Designers, database admins, coders, UX consultants, and individuals from the publishing industry would all be able to contribute towards the design of our journal policy database prototype. In addition, anyone from the publishing industry, or who interacts with the publishing industry (i.e. researchers), would be able to offer comment on the prototypes and/or user test the prototype.

The post Code is Science appeared first on eLife Innovation Sprint 2021.

I hope to create a website that allows users to easily share and view any information they and the community have on the reproducibility of papers. 

Led by Cassio Amorim

Aim

I created the website SciGen.Report to provide a platform to easily share and view any information that researchers may have on the reproducibility of papers.

Information about the reproducibility of papers is scarce in most research fields, due to the difficulty in publishing negative or partial results. Consequently, while graduate school students do perform at least partial replication of works as part of their studies, individual reproducibility information is lost and unavailable. It may take a considerable time for people to be able to discuss the reproducibility of a given paper, usually through discussions in workshops and conferences. This scenario leaves people from other fields alienated to the research status and credibility of a given work, which also leads to serious obstacles to research. 

SciGen.Report’s simplicity reduces barriers for every user, from students to long-career researchers – I hope that a diverse range of users may engage and contribute to the common body of knowledge. Only one submission limited in size is allowed per user, as a way to reduce potential abuses and to keep objectivity. The core principles of this project are diversity, integrity and transparency, and these should sustain every provided functionality and every decision regarding future implementations.

Work at the Sprint

I hope to design a more intuitive interface with little friction, and where researchers, from students to long-career researchers, may feel at ease with posting their own submission. I also hope to understand what could motivate users to contribute their own knowledge to such a platform. Currently, a link to a submitted comment is made available and can be used for references and citations, but I believe more work needs to be done. 

I am looking for…

Contributors with knowledge of UX, UI, design and marketing. Also, people with different backgrounds could help us to share a broader understanding of the role played by reproducibility, whether with positive or negative results. Contributors with knowledge on PHP, CSS, HTML and Javascript may provide technical advice too.

The post SciGen.Report appeared first on eLife Innovation Sprint 2021.

We envision a platform that can help students and early-career researchers identify journals that can offer waivers or subsidies, and how to access them. We seek a platform that will reduce the APC cost barrier for students from resource-poor settings.

Led by Caleb Kibet, Kennedy Mwangi and Jennifer Mutisya

Aim

Adam is an MSc student at a local university in Kenya. He has to work part time to pay his school fees. Adam does the same through his research project to pay for bench fees at a local research institution. Through sweat and long nights, he manages to get a manuscript ready, as he has to publish to graduate. Adam recently attended a seminar where he was introduced to open science. He is excited about his first paper and wants to publish open access. His excitement is cut short when he realises he has to pay a US$3,000 article processing charge (APC) to get his manuscript published. What are his options? Are there publishers that can offer him a waiver or a subsidy? Or, are there some funding opportunities he can tap into for support?

We envision a platform that can help Adam identify journals that can offer him waivers or subsidies, and how to access them; a platform that will point him to funding opportunities to help cover the APC. We seek a platform that will reduce the APC cost barrier for students from resource-poor settings, like Adam. 

Work at the Sprint

We will approach the challenge in levels:

• Convert the LowCostOpenAccess – a resource for people to get information on journals where they can publish at a waived or subsidised APC – to an interactive website
• Prototype a quick page to host the content we already have at LowCostOpenAccess: 
• Build a web scraper to get the data from publisher pages automatically, and existing APIs. We will seek to build upon and take advantage of any existing resource or data that support our vision. 
• Most of the open-access publication funds available are from well-established universities. Are there funding opportunities available for students in lower-income countries? 
• Share the platform with prospective users, seek feedback via a survey, and incorporate the feedback into the platform design. 

We are looking for…

Contributors with expertise in web development and UX, as well as users with experience in publishing and open access to test and provide feedback, and communicators to document and add content to the site. Those with expertise in data science, such as web scraping, would also be welcome.

The post Affordabee: Low-Cost Open Access Publishing appeared first on eLife Innovation Sprint 2021.

Teaching computers how to read articles can bridge the publication-to-knowledge gap, accelerate scientific discovery and save us time to focus on improving research culture.

Led by Tiago Lubiana

Aim

The vast amount of scientific articles produced nowadays makes it nearly impossible to understand and interpret all relevant works. We end up missing essential discoveries and failing to compare findings across the literature. The lack of standardisation makes it harder to discover researchers that are working with any given topic, and it also hinders the precise definitions of research settings needed to ensure reproducibility. This gap affects the everyday life of every researcher, limiting the reach of our hypotheses and discussions, and the information-based decision making that can solve real-world problems.

Work at the Sprint

To integrate knowledge with computers, we need, as a first step, to annotate scientific texts. We will build a prototype that allows the community annotation of scientific texts to Wikidata items. Wikidata is designed as a single system for all concepts, even outside the biological domain. The use of a single database lowers the barrier for editing, likely improving user engagement. The prototype will save the annotations in a format compatible with the EuropePMC annotations framework. 

The design of the tool may employ the Wikidata API to power a user interface to provide candidate matchings to full open texts and abstracts. This organised corpus of Wikidata-annotated texts, after quality control, can be fed to EuropePMC’s system, which displays annotations using the functioning SciLite system.

I am looking for

Contributors skilled in UX and software development, and with domain expertise in natural language processing, annotations and bioinformatics.

The post Annotate them all appeared first on eLife Innovation Sprint 2021.

As a research software engineer, I would like to develop open software that can be cited just like research papers. I would like to submit a software citation to a publication using existing open software tools, in order to make my software citable and trackable to funders and reusable by other researchers.

Led by Sarthak Sehgal

Aim

Despite doing valuable research, research software engineers (RSEs) do not benefit as much from the current research metric system which highly values citations. This is because researchers using open datasets/software/packages are sometimes not aware of the relevant citation practices, or have no access to clear mechanisms to cite software. There is a lack of awareness and appropriate tools which provide citability and desired recognition for software. The Software Citation Project aims to bridge this gap and create a platform to enable RSEs to publish their software by attaching a DOI and a CITATION.cff file with rich meta-data. I believe that providing a seamless experience to the users, along with relevant information highlighting the importance of citability, is a good first step towards better research practices. 

Work at the Sprint

Primarily, I would like to focus on meeting potential users to try out the beta platform, understanding their needs and getting critical feedback. On the technical front, the project could serve the needs of a larger audience using more diverse tools. Extending support from Zenodo and GitHub to include more services such as Zotero, GitLab and BitBucket for the next release is a major goal as well.

I am looking for…

Potential users (RSEs, or any researchers who write code/software) to interact with and get feedback from. Software developers working with JavaScript to work on the web portal as mentioned earlier would also be very helpful, as well as UX/UI designers to help conduct user testing on the web portal’s design and understand user psychology to provide a better experience.

The post The Software Citation Project appeared first on eLife Innovation Sprint 2021.

It remains difficult for consumers of open data to discover, select and compare open-data repositories and platforms. A solution to collate and display this information will provide valuable data for benchmarking exercises, and ultimately help inform consumers. 

Led by Andreiwid Correa and Kellyton Brito

Aim

Open data powered and enabled many initiatives worldwide, usually in the form of data portals or data platforms. However, it remains difficult for consumers of open data to discover, select and compare open-data repositories and platforms: how many data portals can address their specific use case, what are the most used open data software platforms, and how can the level of openness be compared across repositories in different countries? A solution to collate and display this information will provide valuable data for benchmarking exercises, and ultimately help inform consumers. 

Work at the Sprint

At its heart, the solution needs to contain a way to automatically identify and collect open-data sources; it must crawl web pages worldwide which requires a lot of computational resources. To overcome this, we rely on the Common Crawl project, an open repository of web crawl data that makes available a database of raw data containing a freely accessible copy of the textual web. The solution is based on an iterative scan of the Common Crawl URL index on a monthly basis and allows the automatic identification of data portals and the gathering of information about their availability. The solution should then produce open, accessible data ready for reuse by the community, through the development of visualisation platforms and/or APIs. 

We are looking for…

UX and design contributors to help build a web-based system in a responsive way, with a client-side web development background. Contributors with knowledge and interest in open data and/or experience with platforms and mechanisms to publish data would also be very welcome.

The post Crawling data portals for improving research communication appeared first on eLife Innovation Sprint 2021.

We want to provide researchers with an intuitive tool to concisely formulate why a publication is interesting, who it is interesting for, and what the next step should be.

Led by Michiel van der Vaart and Jan Paul Grollé

Aim

The academic community is frequently sharing scientific publications via Twitter and other social media. However, researchers generally fail to specify why we should take notice of a certain publication, who the intended audience is for the new finding, or what the next step would be to advance the knowledge. We want to provide researchers with an intuitive tool to concisely formulate why a publication is interesting, who it is interesting for, and what the next step should be. These insights are shared in a tweet directed at a target audience specified via #hashtags to facilitate knowledge dissemination and utilisation. All shared insights and the responses they spark are stored in an openly available database to generate a thematic research agenda that advances scientific progress by combining the wisdom of diverse crowds.

Work at the Sprint

We envision the work during the Sprint to be divided into three parts:

1. Design and develop a light-weight user interface that prompts people to summarise the most important finding of a paper in one sentence, formulate the next step for this research in one sentence, and indicate the target audience by adding hashtags
2. Test this interface by asking researchers at the Sprint to use it to send a tweet about a publication. We hope that this feedback will validate our preliminary results that tweeting about publications in a more insightful way is a ‘quick-win’
3. Design and develop the software that captures these tweets (and potentially the replies they generate) and stores them in an openly available database. This would generate a ‘crowd-sourced research agenda’ of suggested next steps

We are looking for…

Contributors with expertise in software development, UX and database infrastructure; researchers to test the application by sending a tweet about a publication; and communication to the broader research community to convince them to tweet about publications in an insightful way.

The post Share your insight, inspire the next step appeared first on eLife Innovation Sprint 2021.

We envision a tool to improve citations from software that can be incorporated into other software to record the references used, wherein the code information from those references was applied.

Led by Diego Alonso Álvarez, Valentin Sulzer and Jez Cope

Aim

Software citation is key to research reproducibility, and software is increasingly being published and cited. And herein lies the problem: that software is not accounted for with a standardised method of citing, thereby making it difficult to give credit to the sources it is based on. This means that neither software packages or library dependencies, nor data sources or research papers containing algorithms implemented in that software, are credited, often being difficult to even identify. 

We envision a tool that can be incorporated into software to record the references used, wherein the code information from those references was applied, as well as any other relevant information related to those references – such as specific parameters employed to execute that part of the code. Our solution will also produce a summary of the references in a standardised format, such as Zenodo or citation file format (CFF), and register it with an indexed online repository. Finally, the tool should provide the references used during a particular run of the software, enabling researchers to incorporate that information when publishing their results, supporting its reproducibility.

Work at the Sprint

The Research References Tracking Tool (R2T2) provides a basic proof of concept of what such a desirable package should look like in Python. We would like to bring R2T2 up to a state of development fit for purpose according to the solution described above. Specific issues to tackle include:

1. Implementing the possibility of adding the references in a range of different formats (DOI, plain text, Latex key and so on) to ease the adoption of the tool and range of possible cited objects
2. Recording relevant runtime information to provide a comprehensive report
3. Providing the summaries in a standardised format, which is machine and human-readable, and with the possibility of registering them with an indexed online repository

Moreover, it will be desirable to develop equivalent sister tools for the other common programming languages used in research, such as R, Julia, Fortran or C/C++. 

We are looking for…

Contributors with experience in any programming language commonly used in research: Python to contribute to the existing R2T2; and R, Julia, Fortran or C/C++ to start one of the sister projects. We are also looking for developers of other projects willing to adopt the tool into their own work and guide its development towards a solution that works for them; and experts in open research, citation index systems or online data and software repositories, to help to implement an output format that can be easily used by other third-party tools.

The post Research References Tracking Tool (R2T2) appeared first on eLife Innovation Sprint 2021.

We want to incentivise research software engineers and researchers who develop software to implement the simple recommendations for making software more FAIR, by making their effort and compliance more visible to the rest of the word.

Led by Mateusz Kuzak, Carlos Martinez Ortiz and Jurriaan Spaaks

Aim

The success of the open-science movement relies on researchers being more open and transparent in sharing their methods, analyses and data, such that these can be reused, verified and/or reproduced by a wider audience. The Netherlands eScience Center and DANS launched fair-software.eu with five actionable and practical recommendations that help researchers to make their software more FAIR (Findable, Accessible, Interoperable, Reusable). 

We want to incentivise research software engineers and researchers who develop software to implement these FAIR recommendations, by making their effort and compliance with the fair-software.eu recommendations more visible to the rest of the world. We also want to promote the recommendations to a wider audience. 

Work at the Sprint

Shields badges are a common way to visualise and communicate the status of the software repository. They can easily be included in GitHub READMEs or other web pages. The service supports dozens of continuous integration services, package registries, distributions, app stores, social networks, code coverage services, and code analysis services. We want to implement a Shields badge that will reflect the compliance with the five FAIR-software recommendations, with the goal of increasing visibility for software authors’ FAIR efforts and encouraging curious visitors to learn more about the recommendations.

During the Sprint, we plan to: 

1. Design the shield.io badge, with versions from 0/5 to 5/5 recommendations implemented 
2. Design a way to programmatically measure compliance (whenever possible)
3. Implement the automated measurement 
4. Implement GitHub action that will run the measurements and update the badge based on the results 

We are looking for…

Contributors with skills in design to help us design the badge. Familiarity with sheilds.io, its gh-badges library used to generate badges and javascript, and/or familiarity with GitHub actions and continuous integration will be extremely helpful too.

The post A badge for FAIR software appeared first on eLife Innovation Sprint 2021.

Demystify and democratise academic research and the “hidden curriculum” with an open repository of grant proposals, fellowship applications, and job statements.

Led by Hao Ye

Aim

Academia has not been inclusive and accessible to everyone. In addition to biases along axes of race, gender, geography, institutional prestige and more, there are often unspoken barriers that constrain who can succeed. Applying open principles to research practices has alleviated some of these barriers. However, another facet involves implicit knowledge around how to write and structure grant proposals, fellowship applications and job statements – aspects that are part of the “hidden curriculum” of academic research. This proposal aims to promote diversity and inclusion in research by improving the accessibility to examples of (both successful and unsuccessful) grant proposals, fellowship applications and job statements – this will build on existing open science practices and continue the process of demystifying and democratising research .

Work at the Sprint

This project seeks to expand upon the efforts of Open Grants. By enhancing both the scope and usability of this existing platform, we will open up formerly closed aspects of the research process in a way that supports reproducibility (by enabling reuse and adaptation), and promotes diversity and inclusion (by removing barriers to certain kinds of resources).

I envision three areas of improvement:

1. Improving the process for adding new materials
2. Updating the storage infrastructure; converting to a database and a dedicated application programming interface (API) will improve the scalability of the platform, and facilitate broader usage of the content
3. Updating the front-end interface

I am looking for…

Folks skilled in software development, design and UX, particularly in the area of online database applications. Some familiarity with academic digital spaces, such as scholarly repositories (including Zenodo, Figshare, Dryad) and ORCID would be helpful as well.

The post Expanding Open Grants appeared first on eLife Innovation Sprint 2021.