Category Archives: Tools and Techniques

Tools and Techniques

A Super SoNYC Birthday

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Everyone at last week’s SoNYC event was in a celebratory mood. After we toasted with our festively decorated cupcakes, the floor was turned over to members of the audience to present tools and apps that help them do or communicate science. In addition to the tools and apps presented at the SoNYC event, check out our list of #ToolTales over at Soapbox Science.

Here’s a rundown of last weeks’s presenters:

First up was Richard Wing of Project Bourbon. Frustrated with the lack of clear, effective images and charts to explain scientific ideas, Wing decided to make his own.

Check out their submission to Alan Alda’s flame challenge on their Facebook page.

Project Bourbon is still in its infancy and looking for people to help out with creating content and designing the infrastructure and organization for this future tool. If you’re interested in helping out or in learning more about Project Bourbon, check out their Facebook page or follow them on Twitter: @ProjectBourbon1.

"This should be your home page" - Bora Zivkovic

With all the great science blogs out there and all the blogs out there that don’t have anything at all to do with science, how can one person possibly find the time to sift through them all? As Bora Zivkovic of Scientific American explained, you don’t have to. ScienceSeeker will aggregate posts from science blogs that have been approved and vetted by members of the science blogging community, so you’re sure not to run across someone’s Friday night cat pics.

AstroBetter

Kelle Cruz gave us an intro to her website – Astrobetter – a LifeHacker-esque site geared towards astronomers, but with topics that most scientists would find useful, such as being yourself during an interview, how to speak well in front of others, and whether QR codes are useful for scientific posters.

Pat Gordon and Ashlee Bennett, two graduate students at Columbia University, started Biochemistry Revealed to help scientists explain their research around the Thanksgiving day table. With podcasts and blog posts like “We sequenced the human genome!…now what?” and “Proteins – more than just a good steak”, Biochemistry Revealed is geared toward your average armchair scientists who needs a refresher course in some of the basic concepts of chemistry and biology.

Scienceline is a website featuring the work of NYU students. Rose Eveleth talked about her experience in helping create a Scienceline iPad app. One of the most important things for building an app? Knowing how to use an iPad. Also important was knowing how to differentiate the Scienceline app from the website. For Eveleth, that meant adding special extras and bonus features to the app that the website didn’t have.

The Atavist

The Atavist is an online multimedia magazine that publishes nonfiction stories. However, Olivia Koski gave us the inside scoop into how the Atavist is branching out into becoming a general publishing platform that anyone can use to publish their stories. They are currently looking for beta testers. So, check out their website and see how you can help.

Kendra Snyder, from the American Museum of Natural History, gave us a demonstration of one of the cool apps that AMNH is using to help get people involved and excited about its exhibits. In the app for the exhibit “Beyond Planet Earth”, visitors hold an iPad over icons place throughout the exhibit. The iPad sees the icon through its camera and creates a 3D, interactive image the corresponds to the image, such as the moon, the solar system, and even a lunar elevator.

Contextly

Contextly is a plugin for WordPress created by Ryan Singel of Wired. Contextly helps writers and publishers link their articles to related content.

Science@Columbia

In an attempt to coalesce all the great science being done at Columbia University, Jeff Lancaster created the Tumblr page Science@Columbia. The goal is to build bridges between different departments at Columbia that may otherwise operate independently and provide a cohesive resource for non-Columbia-nites who want to know what kind of science is done there. Check it out for the Secret Science Club events, recently published articles, and current science news.

Musa Akbari, founder of Meritocracy, offered his view of of cloud-reviewed publishing platform. Read Musa’s #ToolTale here to hear more about his idea for Meritocracy.

Science Exchange

What do scientists do when they need an experiment done but don’t have the tools or know-how to do it themselves? Well, as Jeanne Garbarino explained, they can check out Science Exchange, an online science marketplace that connects experiment providers with scientists who need to get experiments done.

Wikipedia

While Wikipedia may not be exactly new, Lane Rasberry, Wikipedian in Residence at Consumer Reports,  presented it in a whole new light. How does a science communicator reach millions of readers, publish on the largest publishing platform in the world, and have your words show up as the #1 hit on Google? Publish on Wikipedia.

Tool Tales: Meritocracy – Cloud-Reviewed Science

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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 here, Benedict Noel’s here, Chris Surridge’s here and Gerd Moe-Behrens’s here.   

Introduction to Tool Tales: Using Science Tools in the Classroom

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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?

This is cross-posted on Soapbox Science. 

My favorite thing about all the online science apps and tools is that they make real science accessible to anyone – even sixth graders.  Last fall, I taught a course through Citizen Schools, an after school program for middle schoolers. Part of the program includes what is called “apprenticeships”, in which people come in and teach something about their job or profession. As a scientist, I decided I wanted to teach the kids about structure-based drug design.

The goal of the class was to teach the kids a little bit about what proteins look like and how they can use that knowledge to design drugs. I wanted to show students that they can do real scientific research, similar to what scientists are doing now. Using HIV-1 protease as our model system, we used the program Pymol to visualize the protein bound to different HIV drugs and decided on what types of changes we could make to those drugs to hopefully make them bind better.

Next, the kids went into the computer lab and drew their new drugs in MarvinSketch (a great, intuitive, easy-to-use chem drawing software). There are a lot of great chem drawing programs out there, but I chose MarvinSketch because it’s free, it’s easy to use, and it has some fun features. The kids got a kick out of using the molecular dynamics feature and seeing their molecules wiggle and dance.

After drawing their drugs, we docked the molecules onto the HIV-1 protease structure using the Autodock/Vina plugin for Pymol. I spent a lot of time looking for a docking software that I thought sixth graders could use, and I picked Autodock/Vina because it’s easy to use, has a decent GUI interface, and works with Pymol, which I already knew how to use. With Autodock/Vina, you take a PDB structure of a protein and a PDB structure of a small molecule, define a binding site, and the program determines and ranks the top ten conformations of the molecule docked onto the protein.

Drug bound to HIV-1 protease (designed by sixth grade student)

The overall goal was to have students look at how current drugs interact with HIV-1 protease, generate hypotheses on how to change the drugs to make them better and then make those drugs with the computer and see if they bind. All the while, the students would be using tools and programs that real scientists use in the lab.

So, did it work? I knew going in that I had my work cut out for me. The concepts of atoms and molecules are so abstract and esoteric that it’s hard to conceptualize them, but using the tools above really helped the kids visualize these things. I know there was some disconnect on what molecules actually are, like how big they are, where they’re found, how they are a part of living things but not themselves living. Also, because we didn’t go into depth about things like salt bridges, hydrogen bonds, and hydrophobic interactions, the “design” part of the structure-based drug design was a little more random than rational.

But for me, the most important lesson that every student walked away with was that they could be scientists and that they could actually help solve the problems of the world.

While I thought that my approach to teach structure-based drug design was kind of clever, it seems that an upcoming version of Fold-it may do something similar, all in one program.

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, Mike Biocchi’s here, Susanna Speier’s here, Derek Hennen’s here, Musa Akbari’s here, Benedict Noel’s here, Chris Surridge’s here and Gerd Moe-Behrens’s here.