Tag: Open data

Ashley Farley of the Gates Foundation: “Knowledge should be a public good.”

Hi Ashley, and thanks for joining us here! Could you start off by letting us know a little bit about your background?

Certainly! I began college aiming for a Zoology degree while working at the University’s library. My love for information grew in proportion to my struggle for mastering Physics and Organic Chemistry. My senior year I transferred disciplines and graduated with a Bachelor of Arts (BA) focused on Library and Information Science. For the next decade, I worked in both public and academic libraries and began pursuing my Masters in Library and Information Sciences from the University of Washington (to be completed this summer. Yay!) Now I have found myself submersed in the realm of scientific knowledge and research dissemination. I find this to be a perfect way to combine all my passions – science, knowledge, and service to others.

Credit: Ashley Farley

When did you first hear about open access and open science? What were your initial thoughts?

The first time I heard about these topics was while interning at the Bill and Melinda Gates Foundation in the Knowledge and Research Services department. My initial thought was “How have I not heard of this before?!”. Having worked in libraries for many years I was familiar with the serials crisis and the importance of research, but I had not been introduced to the Open Access movement. Then I thought, “Of course Open Access should be the norm!”. Knowledge should be a public good.

“Of course Open Access should be the norm!”. Knowledge should be a public good.

What’s it like working for the Gates Foundation? How much of your time do you spend working on ‘open’ related things?

I really love working for the Gates Foundation – it’s providing me with the opportunity, each day, to work towards a greater good. A message that is posted throughout the foundation is “All Lives Have Equal Value” and I take this to heart. This is the first institution where I have been employed to embrace innovation and move initiatives forward fairly quickly. One of our tenets is that we will take risks that others can’t or won’t and I’m proud of this. Currently, I spend about 90% of my time on Open Access. This encompasses internal and external communications, advocacy of our policy, and working with our grantees to make their research open access. We’ve recently joined the newly launched Open Research Funders Group (ORFG) to work with other research funders worldwide to adopt mandates like ours. Together we can create a funding environment where Open Access or even Open Science is the norm. I am beginning to see the impact that my work has on the scientific community and it’s very exciting. We have other partnerships in the works that will be announced soon to continue to support the Open Access movement.

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Xuan Yu, a man with a mission to bring Open Science to the Earth [Sciences]

Part of my job at ScienceOpen is, and this might come as a surprise, advocating Open Science practices. It’s very easy to get bored of my own voice and ideas though, and I love hearing the perspectives and experiences of others. By listening to others about their Open Science adventures, and taking on board what they have to say and learning from them, we become stronger ourselves and as part of a community, and understand how to put things into practice more easily. This is why the Open Science Stars series exists, and why it’s so important! The next interview in the series is with Xuan Yu, and is our first with an Earth scientist, which is very exciting! Enjoy!

Credit: Xuan Yu
Credit: Xuan Yu

Hi Xuan! When did you first hear about ‘open science’? What was your first reaction, do you remember?

When I joined the OntoSoft committee meeting in March, 2015, I was introduced the concept of ‘open science’. I was not convinced by the concept, because there are usually many individual preference-based methods involved in most of geoscience projects.

It seems like much of the global push for open science comes from the Life Sciences. How are things in the Earth Sciences in terms of awareness and solutions?

Earth Sciences are slowing moving towards transparent, reproducible, and open culture. Many funding agencies and publishers have made actions to promote open science.

Can you tell us about some of the strategies you’ve developed for sharing data and software in geoscience? What drives your commitment to this?

I would like to recommend the strategy of transparent publication in geoscience. Sharing data and software with journal articles will draw wide attention and be practical. Because: 1) background information about the data and software has been explained in the article, which increases data transparency, 2) a scientific story in the article will lead readers to the data and software, which promotes the utility of the data. Specifically, there are four key steps in transparent publication of geoscience: persistent, linked, user-friendly, and sustainable (PLUS).

Continue reading “Xuan Yu, a man with a mission to bring Open Science to the Earth [Sciences]”  

Chris Hartgerink: A champion of Open Science

The Open Science Stars series has been one of the most pleasurable aspects for me of working at ScienceOpen, seeing the great diversity of researchers all around the world working to make science a better field to be in. For the latest, we spoke with Chris Hartgerink, a PhD student at Tilburg University in the Netherlands. Chris has a strong background in open research practices, and is a prolific member of the data mining community. Here’s his story!

When did you first hear about ‘open science’? What was your first reaction, do you remember?

Credit: Chris Hartgerink
Credit: Chris Hartgerink

I first heard about Open Science in late 2012/early 2013 during my Masters. My then supervisor (Jelte Wicherts) said to me, “Let’s put all this online”, and I remember thinking this seemed so obvious but that I simply hadn’t considered it before – nor had I been taught about this during my education. This helped multiple puzzle pieces to fall into place. Since then transparent research has been central to all that I do. I also remember asking myself how to do this because it is non-trivial if you simply know nothing about it, and it has been a gradual process since then learning how to share in an easy-to-comprehend way. But it doesn’t have to be perfect from the beginning because open science is more a way of approaching science than it is a checkmark.

What has inspired your dedication to open research? What sort of things do you do on a daily basis to commit to this?

To be honest, what you call dedication is an ethical responsibility in my eyes. The old, opaque way of doing science is based on the analogue age with severely outdated standards. This is irresponsible, just like a current-day astronomer using Galileo’s antique telescope would be irresponsible. This antique telescope gives relatively imprecise measures compared to modern telescopes, so nobody would pay attention to new results based on it. I don’t think the science done with the antique telescope in the old days is invalid, I just think we have to build on the old, create the new, and then use the new. Closed research, as you might call it, is stuck in the old. I would even go so far to say that such unnecessarily (!) closed research obfuscates science and can be deemed pseudo-science. I hardly pay attention to new research that is unverifiable.

The old, opaque way of doing science is based on the analogue age with severely outdated standards.

By the way, when I say irresponsible, I mean irresponsible to others and to yourself. Our work is complex and making your work shareable and understandable to others helps others to understand what you did – including your future self. Transparent research has saved my skin repeatedly.

Continue reading “Chris Hartgerink: A champion of Open Science”  

Data sharing is crucial for genomics research!

Our ongoing ‘Open Science Stars’ series has highlighted some of the vast variety of views, experiences, and facets of open science, and a cadre of great people working to drive real and positive change. This week, we spoke with Fiona Nielsen, who has founded two companies dedicated to the sharing of genomics data! Here’s her amazing story.

Hi Fiona! Thanks for joining us at the ScienceOpen blog. Could you start off by letting us know a bit about your background?

Pleased to join your blog series. 🙂

I am a bioinformatics researcher with a background in computer science. My first degree was a short computer science degree, which I then expanded by studying bioinformatics at the University of Southern Denmark, where I gradually moved more and more into genetics and DNA sequence analysis. After my masters I moved to Nijmegen, the Netherlands where I studied for a PhD in bioinformatics at the NCMLS. During my time as a PhD student, my mother was diagnosed with cancer, and I lost my motivation to work on scientific topics far removed from patient impact. I moved to Cambridge, UK to work for Illumina, and after two years I decided to leave my 9-5 job to start my own project: I founded first the charity DNAdigest and later the company Repositive to enable better data sharing within genomics research.

Cute! Had to share this from the Repositive site (
Cute! Had to share this from the Repositive site (


When did you first become interested in Open Access and Open Science? What was your initial reaction when you heard about it?

I do not recall when I first came across the terms of Open Access and Open Science, but I do recall that I repeatedly came across anecdotes from colleagues that could not access data or results from published papers, and how I looked up to the progressive researchers who would “go all the way” and make all data and results available immediately, even before publication of a paper.

  Continue reading “Data sharing is crucial for genomics research!”  

Julien Colomb on open science and firing lasers at flies

Continuing our ‘open science stars’ series, we’re happy to present Dr. Julien Colomb this week! Julien is a postdoc in Berlin, and we’ve been working together (well, Julien has tolerated my presence..) at Open Science meetups here, which he’s been using to build an active community over the last 10 months or so. He recently published a cool paper in PeerJ and built a new ScienceOpen Collection, so we asked for his thoughts and experience with Open Science!

Hi Julien! Thanks for joining us at the ScienceOpen blog. Could you start off by letting us know a bit about your background?

Hi John. My pleasure to be here. [We’ve known each other for a year and he still can’t spell my name..]

I have been interested in neurobiology since my high school time; I got to work with Drosophila during my Master’s thesis and could then not leave the field. I worked about 10 years on the neuroanatomy and behaviour in the fruit fly larvae and flies in Switzerland, Paris and Berlin. In 2013, I decided to stay in Berlin when the mentor of my second post-doc, Prof. Brembs, moved to Regensburg. In the last 3 years, I have been jumping between different jobs in Prof. Winter groups, I have been wandering in the startup community in Berlin (founding Drososhare GmbH), and trying to foster open science and open data. At the moment, I work half time at the Charite animal outcome core facility, while we work on getting a beta version of the Drososhare product (a platform to share transgenic Drosophila between scientists). I also run the Berlin Open Science Meetup.

Drososhare (Source)
Drososhare (Source)

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In:  Peer Review  

The Peer Reviewers Openness Initiative

Openness in scholarly communication takes many forms. One of the most commonly debated in academic spheres is undoubtedly open access – the free, equal, and unrestricted access to research papers. As well as open access, there are also great pushes being made in the realms of open data and open metrics. Together, these all come under an umbrella of ‘open research’.

One important aspect of open research is peer review. At ScienceOpen, we advocate maximum transparency in the peer review process, based on the concept that research should be an open dialogue and not locked away in the dark. We have two main peer review initiatives for our content: peer review by endorsement, and post-publication peer review.

On the complex web that is Open Research. Source.
On the complex web that is Open Research. Source.

A new project has been launched recently, the Peer Reviewers Openness Initiative (PROI). Similarly to ScienceOpen, is grounded in the belief that openness and transparency are core values of science. The core of the initiative is to encourage reviewers of research papers to make open practices a pre-condition for a more comprehensive review process. You can read more about the Initiative here in a paper (open access, obviously) published via the Royal Society.

Central to the PROI are five simple guidelines:

  1. Data should be made publicly available.All data needed for evaluation and reproduction of the published research should be made publicly available, online, hosted by a reliable third party. [I’m an author; help me comply!]
  2. Stimuli and materials should be made publicly available.Stimulus materials, experimental instructions and programs, survey questions, and other similar materials should be made publicly available, hosted by a reliable third party. [I’m an author; help me comply!]
  3. In case some data or materials are not open, clear reasons (e.g., legal, ethical constraints, or severe impracticality) should be given why. These reasons should be outlined in the manuscript.[I’m an author; help me comply!]
  4. Documents containing details for interpreting any files or code, and how to compile and run any software programs should be made available with the above items.In addition, licensing or other restrictions on their use should be made clear. [I’m an author; help me comply!]
  5. The location of all of these files should be advertised in the manuscript, and all files should be hosted by a reliable third party.The choice of online file hosting should be made to maximize the probability that the files will be accessible for many years, and to minimize the probability that they will be lost for trivial reasons (e.g., accidental deletions, moving files). [I’m an author; help me comply!]

Stephanie Dawson, CEO of ScienceOpen, and Jon Tennant, Communications Director, have signed the PROI, both on behalf of ScienceOpen and independently, respectively, joining more than 200 other researchers to date. Joining only takes a few seconds of your time, and would help to solidify a real commitment to making the peer review process more transparent, and helping to realise the wider goal of an open research environment.

In:  Research  

New ScienceOpen study on the effectiveness of student evaluations of teaching highlights gender bias against female instructors

Student evaluations in teaching form a core part of our education system. However, there is little evidence to demonstrate that they are effective, or even work as they’re supposed to. This is despite such rating systems being used, studied and debated for almost a century.

A new analysis published in ScienceOpen Research offers evidence against the reliability of student evaluations in teaching, particularly as a measure of teaching effectiveness and for tenure or promotion decisions. In addition, the new study identified a bias against female instructors.

The new study by Anne Boring, Kellie Ottoboni, and Philip Stark (ScienceOpen Board Member) has already been picked up by several major news outlets including Inside Higher Education and Pacific Standard. This gives it an altmetric score of 54 (at the time of writing), which is the highest for any ScienceOpen Research paper to date!

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ScienceOpen Author Interview Series – Daniel Graziotin

ScienceOpen Author Interview Series – Daniel Graziotin

Today’s interview comes from another recent ScienceOpen author, Daniel Graziotin. In his ScienceOpen article, “Green open access in computer science – an exploratory study on author-based self-archiving awareness, practice, and inhibitors,” he analyses the results of an exploratory questionnaire given to Computer Scientists. It addressed issues around various forms of academic publishing, self-archiving of research, and copyright. In the following interview with ScienceOpen, Graziotin gives a unique perspective, as a young scientist and as a software and web developer coming to scientific publishing from the world of open software development. His ideas are bound to be interesting to emerging scientists in particular, as he represents a new globally engaged generation of scientific researchers making full use of open knowledge to further innovation. Continue reading “ScienceOpen Author Interview Series – Daniel Graziotin”