Tool Tales – A Short Summary #SoNYC

To celebrate Science Online New York’s (SoNYC’s) first birthday, we have been reminiscing on past events by highlighting some of the key take home messages, linking out to pictures and hearing from the co-organisers. We recently summarised all of the past SoNYC events; you can read the recap of the events from the science communication and outreach strand here, online tools for scientists and digital publishing here and the implicational issues – legal, policy and community here.

SoNYC  encourages audience participation in the discussion of how science is carried out and communicated online. So in order to celebrate our first birthday in an “app-t” syle, we are handing the mic over to the audience; anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun.

To complement the celebrations, over the last two weeks we hosted a series of guest posts on Soapbox Science where a range of scientists shared details about what’s in their online science toolkits.

Summary of the #ToolTales posts

You can follow the online conversation on Twitter with the #ToolTales hashtag. Why not let us know how they compare to the tools that you use in the comment threads?

Hearing from the SoNYC organisers 

To finish our warm-up to the party, we also heard from each of the SoNYC co-organisers.  First up was co-organiser Jeanne Garbarino from Rockefeller University. In her retrospective post, she detailed the birth of SoNYC and how the internet has enabled her to tap into a community she never knew existed.  Next up John Timmer, Science Editor at Ars Technica, explained how the organisers all met and how they decided on the SoNYC format. Finally, Lou Woodley, nature.com’s Communities Specialist, explained the importance of cultivating connections and why SoNYC-style events are important.

It has been a super-SoNYC year and we hope you have enjoyed the conversations, whether it has been in person, online, or via our write-ups and Storifys. SoNYC’s second year has a lot to live up to!

Source: Super-SoNYC cupcakes to celebrate! 

Tool Tales: Leukippos – Synthetic Biology Lab in the Cloud

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Gerd Moe-Behrens has a PhD from the Faculty of Medicine, University of Oslo, Norway.  During a brief Post Doc at the Max Planck Institute for Molecular Genetics, Berlin, Germany his scientific focus was on Induced Pluripotent Stem Cells. This work introduced him to Systems Biology. This was the starting point for his interest in Synthetic Biology with a special focus on biocomputing. He started to join the Apple developer program, focused on dry lab work and work on an Apple platform (xcode, dashcode, objective c, html5, css3, java). He then founded the Leukippos Institute for Synthetic Biology, a research institute solely in the cloud. He has a strong interest to explore novel forms of scientific work on a web platform. His personal research interests are computer assisted design, morphogenesis and cellular computers. Continue reading

Tool Tales: Antibodypedia – Searching for the Perfect Partner

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Chris Surridge is Chief Editor of Nature Protocols and Associate Publisher the Protocol Exchange. He is also involved in a collaboration between NPG and Antibodypedia a database of information about publically available antibodies created by scientists at the Royal Institute of Technology, Stockholm, Sweden.

Antibodies are the workhorses of cell biological research. Take a wander through the research published in any cell biology journal and you will quickly become convinced that almost no research could be done without these adaptable little molecules. Immunoprecipitation, immunolocalisation, immunofluorescence, Elisa, Western blot – it is very difficult to find any research papers in the field that don’t employ at least one of the multitude of antibody based techniques. Continue reading

Tool Tales: Zombal – Outsourcing for Science

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Benedict Noel is an Australian scientific entrepreneur with BSc and BCompSc degrees from the University of Western Australia. He has always worked for startups, and over the past few years he has become instrumental in mediating between outsourcing contractors and local companies. In late 2009, it came to him that there was a gap in the outsourcing sector — science. He launched his scientific and R&D outsourcing company, Zombal, with the goal of bringing this new sector into the public light.

I’ve always had a passion for science and I’ve earned degrees with majors in Geology, Archaeology and Computer Science. However, I’ve discovered that entrepreneurial pursuits bring me the most happiness.

A few years ago my father asked if I could find a freelancer to do some science work for him — physics calculations. After I really struggled to find an ideal candidate using the available freelancing sites, the idea for Zombal was born – an outsourcing site especially for science. The primary goal of the site is to provide a hub for scientists to register for work, displaying their skills through a profile. If you need assistance from a scientist, you can come to the site, post your requirements and then invite particular individuals to place a bid on your proposal. This online hiring process is made simple for both the employer and the scientist. In fact, we want to make the process of connecting like-minded people as easy as possible. Continue reading

Tool Tales: Meritocracy – Cloud-Reviewed Science

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Musa Akbari is an Iranian, born in Turkey, who has lived in the Bay Area for the latter half of his life. He graduated with degrees in Science and Technology Studies and Contemporary Leadership from UC Davis. With a deep understanding of networked systems in the sciences, combined with practical experience in emerging markets in web tech, he felt drawn to the insensible disconnect between how science is done and the technologies available today. He has assumed this opportunity as a personal quest to help facilitate the inevitable shift in scientific peer-review and publishing.  

One may argue that we live in times of expertocracy. Everything around us has its fundamental roots in scientific research; from the materials we use in clothing and furniture to their distribution channels; the food products we consume to our daily medicine; studies that determine economic and political policies to the management of energy resources – nearly everything we know and practice has originated from or supplemented by some scientific inquiry. Ideally, we make policy and business decisions based on the most meritable science, but relentless tension between controversial practices – from fracking to pesticides to mortgage frauds – suggests there is room to improve. But who makes these decisions? Based on what evidence? Do we have consensus among the scientific community? How does the public get a say in these matters?

We place a lot of emphasis and effort on communicating science, but the solution may be simpler than we imagine. Going back to the old adage, medium is the message. The ways in which we do science today are counterproductive to knowledge dissemination. Research is done in isolated groups, reviewed by a few anonymous gatekeepers, and shared with high costs for access – for scientists and the public alike. Scientists are neither compensated nor accredited for reviewing papers, and this process can take months to upwards of a year. Online journal access can be prohibitively expensive for universities and research libraries, whose members rely on current knowledge in their fields. The public doesn’t have free access to scientific literature, 80% of which is funded by their tax dollars. Middleman reinterpretations of research through popular media, without bounds to self-interest, continue to cause dissonance in our practices. Sadly, this antiquated gatekeeper model creates a pass-or-fail process that inevitably results in a publish-or-perish culture.

Self-fulfilling prophecy weakens our ability to calculate opportunity costs; while scientists are bound to an imperfect system, the immediate struggle to prevail overcomes the potential long-term benefits of changing the system itself. As long as science operates in a closed circuit, communicating science will remain an uphill battle. Perhaps there is another way.

There lies an opportunity between science and new web technologies, one that could address the shortcomings of scientific peer-review and publishing and open doors for unprecedented progress in science. A cloud-based platform, maintained by the people for the people, that can pave the way for a stronger and more efficient system of checks and balances, where the most meritable knowledge thrives – a Meritocracy.

Meritocracy is an alternative review and publishing medium, where scientists can connect to researchers with similar pursuits, collaborate at the speed of social networks, and navigate through papers based on peer recommendations and field impact. Peer-review, which implies 2-4 anonymous, opaque evaluations, evolves into cloud review, which implies transparent, post-publication evaluations by large communities of peers. Decentralized communities, formed and maintained by host institutions or research coalitions, self-publish their papers. Users retain full ownership of their work, and papers shared in the public domain are centralized by research field and made freely accessible by all.

Let’s fast-forward to a day when Meritocracy has come to full fruition. Let’s take a hypothetical example of how a scientist could operate on such a platform.

Say you are a scientist and have just written a paper. What do you do next? You upload your paper to your online profile which is populated with your research interests, curriculum vitae, past papers, and more. You are connected to your trusted colleagues or can find other subject-matter experts through a social network of researchers and academics. You can customize access and fair use parameters, send personal requests for review, and share your work in the public domain for cloud review. Other scientists can review your paper, anonymously or otherwise, and these in-depth discussions remain visible to all future viewers. Reviews of your paper can be evaluated by others as well, resulting in a fluid rating score which continually adjusts with newfound knowledge and different perspectives. Collaborators and followers of the page can reject inappropriate or misguided comments and reviews by vote (i.e. 5 collaborators, 4 votes to reject; 100 collaborators, 60 to reject, etc.), enabling the community to moderate their own page.

Your references can be linked directly to the original studies, allowing users to seamlessly inquire deeper into the subject, while supplemental data can be uploaded to provide a full evidence base for your claims.  Reviews can be linked directly to the paper, with your approval, to communicate your points to a wider audience range. Your paper can be cited, quoted, discussed, and shared, all of which help quantify the impact of your work.

Your paper remains in review stage until it has gained sufficient reviews and high ratings to be accredited with the same weight of value as a journal-published paper, and the speed of this process is a result of the community’s interest in your paper topic. Publishing negative results becomes a valuable and appreciated contribution to the field. You can promote your paper in a R&D marketplace where businesses can contact you directly for development opportunities.

Papers are open to the public for comments but you can easily switch views to display only accredited reviews, or only questions, and so on. You can join communities centered around special interest topics or research pursuits and collaborate across geographic and institutional boundaries. A personalized news feed will provide trusted paper recommendations, and keep you updated on topics of personal interest. Over time, you can build a scientific portfolio of all your work, qualified by the community at large, allowing interested parties to evaluate your credibility.

This democratizing of the publishing medium imposes a fundamental shift in culture of science; it relieves the pressure to publish in high impact journals, for the sake of personal reputation, shifting focus to the merit of the paper. Cloud review ties social reputation to academic work, creating a more balanced system of checks and balances against errors, frauds, and political and financial influences. And most importantly, open access to scientific knowledge resolves half the battle in communicating science.

60 years ago, print and mass distribution was the most effective way to ensure the integrity and widespread exposure of knowledge. Over 20,000 articles are released each year, and that’s roughly 20% of the research we do. Privatized review and print publishing pose limitations in an age where we are capable of managing high flows of information.

Today knowledge is digital. We have knowledge management software and virtually unlimited storage; we have a democratized web space and worldwide internet access; we have social networks and collaboration tools; we have secure information exchanges and policies that protect proprietary rights. Every conceivable technical circumstance for a 21st century review and publishing system is in place, and the will of the people is the final domino.

Today, Meritocracy is only an idea. Tomorrow, we’ll see what unfolds.

If you’d like to get involved, join our community at www.meritocracyhq.com.

You can follow the online conversation on Twitter with the #ToolTales hashtag and you can read Mary Mangan’s Tool Tale here, Dr Peter Etchells’s Tool Tale here, Alan Cann’s here, Jerry Sheehan’s here, Boris Adryan’s here, Anthony Salvagno’s here, Daniel Burgarth and Matt Leifer’s here, Zen Faulkes’s here, Jenn Cable’s here , Mike Biocchi’s here, Susanna Speier’s here, Derek Hennen’s hereBenedict Noel’s hereChris Surridge’s here and Gerd Moe-Behrens’s here  

Tool Tales: Meritocracy – Cloud-Reviewed Science

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Musa Akbari is an Iranian, born in Turkey, who has lived in the Bay Area for the latter half of his life. He graduated with degrees in Science and Technology Studies and Contemporary Leadership from UC Davis. With a deep understanding of networked systems in the sciences, combined with practical experience in emerging markets in web tech, he felt drawn to the insensible disconnect between how science is done and the technologies available today. He has assumed this opportunity as a personal quest to help facilitate the inevitable shift in scientific peer-review and publishing.  Continue reading

Tool Tales: Project Noah – A Community for Nature Lovers

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Derek Hennen is currently an undergrad studying Biology and Spanish at Marietta College, he will be graduating in a few weeks.  After he graduates, he will be working with a watershed organization in Marietta, Ohio called Friends of the Lower Muskingum River as an AmeriCorps VISTA. Derek is focused on communicating knowledge about insects to the general public through his blog, Normal Biology and through public talks. He plans to continue his insect research at graduate school in the future. Continue reading

Tool Tales: Don’t completely write off Pinterest!

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Susanna Speier currently works in social media and digital journalism. Her writing credits include Scientific American, Newsweek/The Daily Beast and The Denver Post and her science themed plays have been produced HERE Arts Center, The Tenri and Galapagos Arts Space. She has a Masters in Playwriting from Brooklyn College, C.U.N.Y. and a Bachelors from Hampshire College. She has also created a couple dozen Pinterset boards for her social media clients in the fashion and real estate industries. The disproportionate amount of attention Pinterest users dedicated to fashion and decorating is probably her fault.

Continue reading

Tool Tales: Can Games Help Learning?

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Mike Biocchi is currently a PhD student focusing his research on Education Technology and E-learning. His research is aimed at using video games as an educational tool inside the classroom, instead of a means of just entertainment. Mike has an  MSc in Computer Games Technology and is the founder and owner of Chamfered Technology. He is also the Academic Specialist at Algoma University in the IT Department and a part-time faculty member at Algoma University with the Computer Science Department.  Continue reading

Tool Tales: Using Science Tools in the Classroom

Science Online New York (SoNYC) encourages audience participation in the discussion of how science is carried out and communicated online. To celebrate our first birthday, we are handing the mic over to the audience so that anyone who would like to participate will get five minutes to show off their favourite online tool, application or website that makes science online fun. To complement the celebrations, we’re hosting a series of guest posts on Soapbox Science where a range of scientists share details about what’s in their online science toolkits.  Why not let us know how they compare to the tools that you use in the comment threads?

Jenn Cable  received a PhD in Biochemistry in June 2011 and since then has been working towards becoming a science writer. She currently writes regularly on nature.com’s New York Blog and also works as a medical writer, developing materials for new drugs. Continue reading