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Author: Jon Tennant

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However, the arXiv is not peer reviewed in the formal sense.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?

Continue reading “What if you could peer review the arXiv?”  

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.

Continue reading “Open science stars: An interview with Dr. Gal Schkolnik”  

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.

Continue reading “Open Science Stars: An interview with Daniel Shanahan”  

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)

Continue reading “Open science stars: An interview with Dr. Joanne Kamens”  

10 simple ways you can interact with ScienceOpen

Doing peer review is tough. Building a Collection is tough. Both are also time consuming, and academics are like the White Rabbit from Alice in Wonderland: never enough time!

So while the benefits of open peer review and building Collection need to be considered in the ‘temporal trade off’ world of research, what are some other things researchers can do to help advance open science with us?

Here’s a simple list of 10 things that take anything from a few seconds to a few minutes!

You can find this on every single article record (11 million!) and interact in a multitude of ways.
You can find this on every single article record (11 million!) and interact in a multitude of ways.
  1. Rate an article. You don’t have to do a full peer review, but can simply provide a rating. Come back later and provide a full review!
  2. Recommend an article. Click, done. Interested researchers can see which articles are more highly recommended by the community.
  3. Share an article. Use social media? Share on Facebook, Twitter, Google+, email, or further on ScienceOpen.
  4. Comment on an article. Members with one item in their ORCID accounts can comment on any article.
  5. Follow a Collection. See a Collection you like (like this?) Click, ‘Follow’, done.
  6. Comment on a Collection. Like with all our articles, all Collection articles can be commented on, shared, recommended and peer reviewed.
  7. Become a ScienceOpen member. It’s not needed for many of the functions on our platform, but does mean you can engage with the existing community and content more. Register here!
  8. Have you replicated someone’s results? Let them know that in a comment!
  9. Think someone’s methods are really great? Let them know in a comment!
  10. Did someone not cite your work when they should have? Let them know in a comment!

All articles can be commented on. All you need to have is a membership, and an ORCID account with just one item. Easy! Commenting can be as short and sweet or long as you like. But sometimes a comment can be worth a lot of researchers and communities, just in terms of offering new thoughts, perspectives, or validation. Also, comments are great ways for junior researchers to engage with existing research communities.

From a Collection on Perspectives in Scholarly Publishing.
From a Collection on Perspectives in Scholarly Publishing.
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)

Continue reading “Use the Force..”  

In:  ORCID  

ORCID goes national in Germany

At ScienceOpen, there’s nothing more we like than good news for open science! That’s why we’re happy this week to see ORCID announcing a new partnership with the DFG, the German Research Foundation and major government funding body here, to support increased ORCID adoption in Germany.

The aim of this partnership is to standardise and integrated information that is currently distributed throughout more than 230 systems and databases in Germany. By adopting ORCID, this will support German universities and research institutes in implementing ORCID in a co-ordinated and sustainable approach.

orcid-hero-logo

“Thanks to the financial support from the Deutsche Forschungsgemeinschaft we have now the opportunity to promote the use of ORCID in Germany. This is a strong signal for ORCID in Germany,” says Roland Bertelmann, head of the Library and Information Services at the German Research Centre for Geoscience (GFZ).

ORCID is a critical part of research infrastructure, acting as a unique identifier for researchers, and a sort of LinkedIn style profile with your published research, and educational and professional histories embedded, and partnered with tools such as CrossRef/Scopus to make content integration easy and automated.

At ScienceOpen, we’ve implemented ORCID across our platform since day 1, and are part of a major publisher-wide initiative for it. ORCID is used for:

  • Getting credit for peer reviews and Collections, which have CrossRef DOIs so automatically get picked up by ORCID;
  • Quality control for peer review, as we require a minimum of 5 ORCID items to perform formal public peer review;
  • Integrating your profile, as we facilitate simplified logging in and registration through ORCID;
  • An ORCID is required to publish with us too, so we know who you are!

This of course now means that engaging with the ScienceOpen platform for researchers in Germany just became a lot easier! Lucky them!

In:  Peer Review  

Rapid publishing and open peer review accelerating research communication in times of crisis

The Zika virus is an international public health emergency, as declared early on in February by the World Health Organisation. As such, it is critical that the global research community help combat this threat as rapidly and efficiently as possible. This is a case when science can quite literally save lives.

Recently, an article on the host-vector ratio in the Zika virus was published on the arXiv, a platform for articles often called ‘preprints’. This means that the work has not yet been peer reviewed, and is also not available to comment on the arXiv itself due to functional constraints. The paper is stuck in the hidden, timeless limbo of peer review until its eventual emergence as a paper or ultimate rejection.

Continue reading “Rapid publishing and open peer review accelerating research communication in times of crisis”  

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.

Continue reading “Collections as the future of academic-led journals”