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Tag: Open Science

Bastian Greshake – “At least no one is seriously using MatLab”

The latest Open Science Stars interview couldn’t be better timed, as I’m sitting here with the interviewee, Bastian Greshake at OpenCon in Washington DC! Let’s get right to it!

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

Sure! Right now I’m working on my PhD in bioinformatics at the University of Frankfurt, the city in the middle of Germany that is famous for having a more or less working airport. Before I transferred into being an armchair/standing desk biologist I did a Master’s degree in Ecology & Evolution. Much of my, maybe let’s say “traditional”, research is about how evolution has shaped the genomes of the funny living things around us. And then there’s the whole open* shebang, which we’ll probably talk about later.

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

I’m not really sure whether it was before or during my undergrad studies. I was certainly experimenting with open source software since I was 15 or so. For the open access-part I at least vividly remember one of the computational biology nerds sporting an open access-shirt, so I guess that way of advertising works. In any case, in my naivety I was puzzled and shocked that open science and science aren’t the same thing yet (c.f. this), as I would have assumed that academics would be progressive, being on the frontier of knowledge and all (boy, was I wrong!).

What is the state of ‘open science’ in the field of bioinformatics? Do you think it’s progressing faster or more frustratingly slower than other fields?

Bioinformatics is a pretty huge field, so I don’t really dare to speak for all of it. But at least for the part that I’m meddling in I think we’re doing a pretty good job open science-wise. Much of the data people generate is ending up in open repositories, virtually everything is programmed in open source programming languages and much of the written code ends up being open sourced as well. And there are some decent open access journals, with pre-prints becoming more and more accepted as well. Of course, it’s not perfect yet. Many people still seem to have a hard time to resist the siren song of Nature/Science publications and unfortunately it’s also the case that people still use and publish closed source and commercial software for their analysis. But hey, at least no one is seriously using Matlab.

Many people still seem to have a hard time to resist the siren song of Nature/Science

Continue reading “Bastian Greshake – “At least no one is seriously using MatLab””  

“It’s so very broken.” Rachael Dunlop on the state of scholarly communications

Continuing the awesome Open Science Stars series, we spoke with Dr. Rachael Dunlop about her thoughts on scholarly communications. Rachael is such an awesome scientist, she has her own Wikipedia page!

Hi Rachael! Thanks for joining us here. Could you start off by letting us know a little bit about your background?

dr_rachie_qed2013
Rachael Dunlop at QED 2013 in Manchester UK. CC BY SA 3.0 (Source)

I was a late starter in science, having worked in graphic design and advertising as my first career. I went to uni aged 26 to get a science degree and emerged 8 years later with a PhD in Cell Biology. I originally planned to become a Virologist but my Microbiology lecturer was so awful, I switched to Toxicology. Funnily enough, I’d never done any Biology in high school so in first year uni, I had to borrow my sister’s year 12 text books to teach myself the basics of Biology – and now I’m a Biologist.

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

I can’t really recall but it would have been around the time I first started publishing and became aware that if you paid an exorbitant fee, then people could read your papers for free. Of course, researchers never ever have a spare USD3000 to throw around on publishing so it just always seemed out of my reach. It’s a great idea if you can afford it. As for open science, ideas are currency in research so there was never any discussion about participating in an open system.

Continue reading ““It’s so very broken.” Rachael Dunlop on the state of scholarly communications”  

How to start an Open Science revolution! An interview with patient advocate, Graham Steel.

Continuing our Open Science Stars interview series, today we’re happy to bring to you Graham Steel, a relentless campaigner for all things Open!

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

For 25 years, my background (as in day job) was dealing with insurance claims for various insurers, legal firms and service providers. In my spare time as of around 2001, I became involved in research/science outreach and as of now, I would class myself as an open science enthusiast. From Jan 2015 – August 2016, I acted as Community Manager (then Social Media Manager) for ContentMine.

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

In order, I first heard about open access late 2006, open science the following year and then open data. My initial thoughts were that all these entities were much needed and refreshing alternatives to all that I had seen or read about such topics up until then, i.e., closed access, prohibitive paywalls, “data not shown” etc.

You’re what some people call a ‘Patient Advocate’ – what is that, and what’s the story there?

The terms Patient Advocate and Patient Advocacy broadly speaking can mean a number of things. By definition, “Patient advocacy is an area of lay specialization in health care concerned with advocacy for patients, survivors, and carers”. For myself personally, this began in 2001 and mainly concerned bereaved relatives and then patients and their family members. See here for further details.

You relentlessly campaign for various aspects of open science – what drives you in this?

My means of background, I would say with certainty that during the period of around 2008 – 2011, the (sadly now deceased) social media aggregator site Friendfeed was the space in which the foundations for a lot of my current thinking were set out. Prior to that, having already been primed with open access and open data, that’s pretty much where open science really took off in earnest. Science and indeed research in the open is without question the way forward for all.

Science and indeed research in the open is without question the way forward for all.

Continue reading “How to start an Open Science revolution! An interview with patient advocate, Graham Steel.”  

In:  Aggregation  

New partnership with PeerJ

Today, we’re pleased to announce a new partnership with the Open Access publisher PeerJ! We are all  very excited to have PeerJ joining us as one of the leading and most innovative open access publishers, and we are happy to see them continuing to help push the curve for scholarly communication.

You can read the press release here and access all the new content here.

Jason Hoyt, co-founder and CEO of PeerJ said “Computer Science has traditionally been published in conference proceedings, so an Open Access journal is a relatively new scholarly channel, but one that we believe the community is ready to embrace. To get there though, Open Access needs more visibility and that’s why we’re thrilled to be working with ScienceOpen.”

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Brill content now live at ScienceOpen

Recently we made the announcement that we were partnering with Brill, a major publisher in the Humanities and Social Sciences for more than 300 years, and who publishes more than 250 journals and 1000 books and reference works each year.

The journals now indexed on our site, and some of the selected articles are:

  1. Indo-European Linguistics, a fully open access journal devoted to the study of the ancient and medieval Indo-European languages:
    1. Dark matter (link)
    2. Using stem suppletion for semantic reconstruction: The case of Indo-European modals and East Baltic future tense formations (link)
    3. Borrowing, Character Weighting, and Preliminary Cluster Analysis in a Phylogenetic Analysis of the Ancient Greek Dialects (link)
    4. Sonority Sequencing Violations and Prosodic Structure in Latin and Other Indo-European Languages (link)
    5. Accent in Thematic Nouns (link)
    6. Reconstruction Syntactic Variation in Proto-Indo-European (link)

  2. Journal of Greek Linguistics, a fully open access journal dedicated to the descriptive and theoretical study of the Greek language:
    1. On the theoretical implications of Cypriot Greek initial geminates (link)
    2. Subject-verb agreement with coordinated subjects in Ancient Greek (link)
    3. Greek phonetics: The state of the art (link)
    4. Perceptions of difference in the Greek sphere: The case of Cyprus (link)
    5. Morphology in Greek linguistics: The state of the art (link)
  3. Language Dynamics and Change, an international peer-reviewed journal that covers both new and traditional aspects of the study of language change:
    1. On some problematic aspects of subjectification (link)
    2. Correlates of reticulation in linguistic phylogenies (link)
    3. Some principles on the use of macro-areas in typological comparison (link)
    4. A pipeline for computational historic linguistics (link)
    5. Using phylogenetic networks to model Chinese dialect history (link)
    6. Molecular perspectives on the Bantu expansion: A synthesis (link)

Continue reading “Brill content now live at ScienceOpen”  

In:  Aggregation  

New journals coming to ScienceOpen!

A month ago, we launched a new competition for ‘platinum open access’ journals – those which are fully open access and do not charge an APC (article-processing charge). We called this ‘hassle free indexing’, because that is precisely what we’re offering!

The response from the open publishing community was fantastic, and today we’re pleased to announce the winners of the first round!

The following journals will all become part of our next-generation indexing and discovery platform:

  1. JLIS.it
  2. Magnificat Cultura i Literatura Medievals
  3. Algerian Journal of Natural Products
  4. Matters and Matters Select
  5. Informationspraxis
  6. Izquierdas (revista)
  7. Journal of Paleontological Techniques

On top of this, two of the journals will receive a free promotional collection with us! These are Magnificat Cultura i Literatura Medievals, representing the humanities and social sciences (HSS), and Matters, Matters Select representing the Science, Technology, Engineering, and Medicine (STEM) fields.

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In:  Peer Review  

The winner of our Peer Review Week 2016 competition

For Peer Review Week 2016, we set a simple competition for you all, to publicly peer review one of 25 million research articles on our platform. This fitted perfectly with the theme this year of ‘Recognising Review’, as every single peer review conducted with us is published openly and creditable through the application of a CC BY license, which enables the unrestricted sharing and re-use of the reviews providing that attribution is given.

We’re happy to announce that Lauren Collister was the winner this year, and a t-shirt is on your way!

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Lauren performed a civil, constructive, and detailed peer review of a paper entitled Crowdsourcing Language Change with Smartphone Applications. This article is also part of our Language Change collection, created by George Walkden.

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We now have 118 open post-publication peer reviews on our platform. Each one is citable with CrossRef DOIs and can be interlinked with PublonsORCID, and ImpactStory, helping to build you profile as a researcher. This is a practical example that this form of peer review works!

Dasapta Erwin Irawan: The state of Open Science in Indonesia and how to drive change to make research better for everyone

Full steam ahead with our incredible Open Science Stars! We hope you’ve been enjoying it so far, and today we’re bringing you Dasapta Erwin Irawan, a a researcher based in Indonesia at the interface between Engineering, Hydrogeology and Geoscience, and an avid open science supporter. Enjoy his story!

When did you first hear about ‘open science’? What was your first reaction, do you remember?
It’s kind of funny, I heard it first from you :). (Ed: *sniff*) It was one of your blog post in 2012 Relocation, and a chance to try some open science-ing that gave me ideas of sharing my results as fast as I can and as wide as I can. I had finished my PhD when I first read it and your posts on EGU blog. There I noticed your hash tags ‘#OpenPhD` then followed it. I wasn’t serious in using my Twitter handle for academic purposes back then. My first reaction was, to make all my published papers available online, posted them all on my ResearchGate account and my blog.

You have a very strong commitment to open science. What is it that drives this for you?

My strong commitment has been built by seeing so many other doing the same thing. In Indonesia, where not many universities have subscription to major journals, open science could be the answer of what we’ve been looking for. Everybody here keeps saying to submit papers to major paywalled journals, as they have good reputation and indexed by WoS or Scopus, while it should not be that way. What we need in Indonesia is to keep writing, write more in English and find a way to make it easier to be found and accessible by others, as if it was indexed by WoS and Scopus. And I see by using the latest free and open source services, we can do that.

In Indonesia, where not many universities have subscription to major journals, open science could be the answer of what we’ve been looking for

Continue reading “Dasapta Erwin Irawan: The state of Open Science in Indonesia and how to drive change to make research better for everyone”  

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]”  

In:  Peer Review  

Recognition for Review is focus for Peer Review Week 2016

To honor and celebrate peer review, a group of organizations is working collaboratively to plan a week of activities and events. The group is delighted to announce that the second annual Peer Review Week will run from September 19- 25, 2016.

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This year’s theme is Recognition for Review, exploring all aspects of how those participating in review activity – in publishing, grant review, conference submissions, promotion and tenure, and more – should be recognized for their contribution.

Continue reading “Recognition for Review is focus for Peer Review Week 2016”