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Tag: Open Science

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  

Honing your peer review skills with ScienceOpen

I remember my first peer review. An Editor for a well-respected Elsevier journal in Earth Sciences emailed me during the second year of my PhD, asking me to peer review a paper for them. I hadn’t published anything by this point of my PhD, and had received no formal training in how to peer review papers. I initially declined, but was pretty much coerced into doing it, despite my resignations. “It’ll be great training and experience”, I was told. Go on. Go on go on go on go on go on. In the end, I did the review, but got my supervisor to check it over to make sure I was fair, thorough, and constructive.  I remember him saying “This is surprisingly good!”, and thinking ‘Thanks..’. But his response was more because it was my first peer review, without any training in how to do it, rather than anything to do with my ability as a scientist. And rightly so – why should I have been expected to do a good job of peer review at such an early stage in my career, and with no formal training?

From Father Ted. Sorry for non-Brits.
From Father Ted. Sorry for non-Brits.

I wonder then how many other PhD students are told the same, and thrown into the deep end. ‘Peer review for this journal and receive fame and glory. It doesn’t matter how well you do it, as long as you do it.’

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Open Science Stars: Ernesto Priego

We’re continuing our series on highlighting diverse perspectives in the vast field of ‘open science’. The last post in this series with Iara Vidal highlighted the opportunities of using altmetrics, as well as insight into scholarly publishing in Brazil. This week, Ernesto Priego talks with us about problems with the scholarly publishing system that led him to start his own journal, The Comics Grid.

There was no real reason to not start your own journal as an academic, to regain control of our own work and to create, disseminate and engage with scholarship in a faster, more transparent, fairer way.

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

I was born in Mexico City. I am Mexican and I have British nationality too. I studied English Literature at the National Autonomous University of Mexico (UNAM) where I also taught and was part of various research projects. I came to the UK to do a master’s in critical theory at UEA Norwich and a PhD in Information Studies at University College London. I currently teach Library and Information Science at City University London.

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

I cannot recall exactly. I think I first encountered the concept of ‘open access’ via Creative Commons. I was a keen blogger between 1999 and 2006, and I remember that around 2002 I first came across the concept of the ‘commons’. I think it was through Lawrence Lessig that I really got interested into how scholarly communications were incredibly restrictive in comparison to the ideas being discussed by the Free Culture movement. Lessig’s Free Culture (2004) changed things for me. (For more background I recently talked to Mike Taylor about why open access means so much to me in this interview).

We need to think about the greater good, not just about ourselves as individuals.

You run your own journal, The Comics Grid – what was the motivation behind this?

Realising how difficult and expensive it was to access paywalled research got me quite frustrated with scholarly publishing. When I was doing my PhD I just could not understand why academics were stuck with a largely cumbersome and counter-intuitive system. The level of friction was killing my soul (it still does). It just seemed to me (now I understand better the larger issues) there was no real reason to not start your own journal as an academic, to regain control of our own work and to create, disseminate and engage with scholarship in a faster, more transparent, fairer way. I’ve said before that often scholarly publishing feels like that place where academic content goes to die: the end of the road. I feel publishing should be a point of departure, not the end.

Credit: Ernesto Priego
Credit: Ernesto Priego

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Pimp my search engine

Search engines form the core of discovery of research these days. There’s just too much information out there to search journal by journal or on a manual basis.

We highlighted in a previous post the advantages of using ScienceOpen’s dual-layered search and filter functions over others like Google Scholar. Today, we’re happy to announce that we just made it even better!

Say you want to search all of PeerJ’s content. Pop ‘PeerJ’ into the journal search, and it’ll come up with all their content, as it’s all indexed in PubMed. Hey presto, there you have 1530 papers, all with full texts attached. Neat eh! And that will update as more gets published with PeerJ, so you know what to do.

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But that’s a lot of content. What you’ve just discovered is the PeerJ megajournal haystack. We want to filter out the needles.

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What if you could peer review the arXiv?

What is the arXiv?

The arXiv is a server that hosts ‘eprints’ or ‘preprints’ of research papers, and is a key publishing platform for many fields, particularly physics and mathematics. Founded back in 1991 by Paul Ginsparg, it currently hosts over 1 million research articles, with more than 8000 submissions per month!

Despite now being in the running for 25 years, the arXiv still represents one of the greatest technological innovations to utilise the Web for scholarly communication.

While the majority of the content submitted to the arXiv is subsequently also submitted to traditional journals for publication, there is still content which never goes beyond its confines. Irrespective of this, communities engaged with the arXiv still cite articles published there, whether or not they have been formally published in a journal elsewhere.

This is the whole purpose of the arXiv: to facilitate rapid peer-to-peer communication so that science accelerates faster. The fact that all articles are publicly available is incidental, and just happens to be a topic of major interest with the growing open access movement.

The growth of the arXiv (Source)
The growth of the arXiv (Source)

However, the arXiv is not peer reviewed in the formal sense. It is moderated, so that junk submissions can be removed, or manuscripts recategorised, but it lacks the additional layer of quality control of traditional peer review.

So while some might think this poses a risk, ask yourself this question: do you re-use articles critical to your research without making sure that you have checked and understand the research to a sufficient degree that you can appropriately cite it? Because that’s peer review, that is, and it applies irrespective of whether an article has already been peer reviewed or not.

How do you peer review the arXiv?

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Open science stars: An interview with Dr. Gal Schkolnik

Last week, we kicked off a series interviewing some of the top ‘open ​scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’re bringing you another open science star, Dr. Gal Schkolnik, who recently published a really cool Collection with us on the bacterium Shewanella. Here’s her story!

Hi Gal! So can you tell us a bit about your research background, and how you originally got interested in science?

I did my BSc in Chemistry at the Tel Aviv University and my MSc at the Weizmann Institute, analyzing  the chemical composition of deforestation-fire smoke from the Amazon, where farmers and corporations yearly set hectares of rainforest on fire for agriculture and pasture. For my PhD at the Technische Universitaet Berlin I measured the electric fields at protein surfaces and self-assembled monolayers. Now I’m researching Shewanella, an electroactive bacterium that can transfer electrons across its outer membrane. As you can see, I always start on a completely new field, because my greatest passion in life is acquiring knowledge – so learning something new is my favorite kind of challenge. I’m basically just a kid who never got over the “why” stage, haha. Plus I had some very inspiring teachers at school – two wonderful women who nurtured my natural tendency to go deep in pursuit of answers to the hardest questions.

People who have no access to journal subscriptions can use ScienceOpen to gain more knowledge about electroactive bacteria and their possible applications.

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Open Science Stars: An interview with Daniel Shanahan

Last week, we kicked off a series interviewing some of the top ‘open ​scientists’ by interviewing Dr. Joanne Kamens of Addgene, and had a look at some of the great work she’d been doing in promoting a culture of data sharing, and equal opportunity for researchers. Today, we’ve got something completely different, with Daniel Shanahan of BioMed Central who recently published a really cool PeerJ paper on auto-correlation and the impact factor.

Hi Daniel! To start things off, can you tell us a bit about your background?

I completed a Master’s degree in Experimental and Theoretical Physics at University of Cambridge, but must admit I did my Master’s more to have an extra year to play rugby for the university, rather than a love of micro-colloidal particles and electron lasers. I have always loved science though and found my way into STM publishing, albeit from a slightly less than traditional route.

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Open science stars: An interview with Dr. Joanne Kamens

 

Open science is a rapidly evolving field, with a huge diversity of actors involved. We want to highlight some of the superstars helping to spearhead the evolution of scholarly communication, who are real positive forces for change. The first of these is with Joanne Kamens PhD, who currently is the Executive Director for Addgene, a repository for the life sciences. We asked her about open science, the impact this can have on diversity in research, and the value of repositories. Here’s her story!

Hi Joanne! So can you tell us a little bit about your background to get things started?

After graduating University of Pennsylvania I went directly to graduate school in the Harvard Medical School Division of Medical Sciences where I received a PhD in genetics. For you historians, it was the first year that the Division existed allowing students to move around PIs in many departments.  I defended my thesis while 6 months pregnant and had my son while still working in that lab. I had a great mentor in Dr. Roger Brent (now at the Fred Hutchinson Center in Seattle).  I studied transcription using yeast and helped demonstrate that an acidic domain of the Rel protein was activating when brought in proximity to the promoter region. Again for historical perspective, PCR was invented while I was in grad school and I got to beta test the first MJ research PCR machine (M worked on my floor) which had no outsides. Roger Brent’s lab was one of the labs that created the yeast two-hybrid screening system and I have always been a lover of molecular biology technology which serves me well at Addgene.

How does PCR work? (Source)
How does PCR work? (Source)

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In:  Collections  

Use the Force..

We have new Collections coming out of our ears here at ScienceOpen! Last week, we saw two published on the bacterium Shewanella, and another on the Communication Through Coherence theory. Both should represent great platforms and resources for further research in those fields.

The latest is on the diverse field of Atomic Force Microscopy. We asked the Editor, Prof. Yang Gan, to give us a few details about why he created this Collection.

Background

This collection is to celebrate the 30th anniversary of atomic force microscopy (AFM). March 3, 1986 saw publication of the land-marking paper “Atomic force microscope” by G. Binnig, C. G. Quate and C. Gerber (Phys Rev Lett, 56 (1986) 930-933, citations >8,800) with the motivation to invent “a new type of microscope capable of investigating surfaces of insulators on an atomic scale” with high force and dimension resolution. This can be used to measure local properties, such as height, friction, and magnetism, so has massive implications for science.

Since then, AFM has given birth to a large family of scanning probe microscopy (SPM) or SXM where X stands for near-field optical, Kelvin, magnetic, acoustic, thermal, etc. More than 100,000 journal papers, ~6,000 papers/yr since 2008, have been published if one searches the Scopus database with “atomic force microscopy” or “force microscope”. On ScienceOpen, there are over 6,000 article records if one searches using the keywords “atomic force microscopy” too. Nowadays, many disciplines — physics, chemistry, biology, materials, minerals, medicine, geology, nanotechnology, etc — all benefit greatly from using AFM as an important and even key tool for characterization, fabrication and processing.

AFM setup. (Source)
AFM setup. (Source)

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In:  Other  

Collections as the future of academic-led journals

ScienceOpen Collections are thematic groups of research articles that transcend journals and publishers to transform how we collate and build upon scientific knowledge.

What are Collections

The modern research environment is a hyper-dimensional space with a vast quantity of outputs that are impossible to manually manage. You can think of research like a giant Rubik’s cube: you have different ‘colours’ of research that you have to mix and match and play around with to discover how the different sections fit together to become something useful.

CC BY-SA 3.0,  Booyabazooka (Wikipedia)
CC BY-SA 3.0, Booyabazooka (Wikipedia)

We view Collections as the individual faces of a Rubik’s cube. They draw from the vast, and often messy, pool of published research to provide an additional layer of context and clarity. They represent a new way for researchers to filter the published record to discover and curate content that is directly relevant to them, irrespective of who published it or what journal it appears in.

Advantages of Collections

Perhaps the main advantage of Collections to researchers is that they are independent of journals or publishers and their branding criteria. Researchers are undoubtedly the best-placed to assess what research is relevant to themselves and their communities. As such, we see Collections as the natural continuing transformation of the concept of the modern journal, acting in almost full cycle to return them to their basic principles.

The advantage of using Collections is that they provide researchers with the power to filter and select from the published record and create what is in essence a highly-specialised virtual journal. This means that Collections are not pre-selective, but instead comprise papers discriminated only by a single criterion: research that is relevant to your peers, and also deemed relevant by them.

Filtering for Collections occurs at different levels depending on scope or complexity of research. For example, Collections can be designed to focus on different research topics, lab groups or research groups, communities, or even departments or institutions. Collections can also be created for specific conferences and include posters from these, published on ScienceOpen. You define the scope and the selection criteria.

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