This new environment is scalable to support the future growth of the journals, flexible in that it can store any type of data/content, built to minimize downtime, much easier for developing new features and best of all, it makes the journal websites perform much faster.

The migration to New Hope occurred over a 3 day period in November and New Hope officially went into production on November 14. This migration was the culmination of months of development and testing. The migration was completely seamless and users experienced no downtime!

Three weeks after the migration to New Hope, we can show that the new platform really did enhance our journal’s performance. For example:

• Average load time of this PLoS ONE article went from 4 seconds to 0.8 seconds.
• Nightly indexing of article data from Mulgara to Solr used to take 3-6 hours. From MySQL to Solr, the indexing now takes 24 minutes.

Warmest congratulations to the New Hope development team (and our intrepid Linux systems administrator) for building a streamlined new home for the PLoS Journals!

Update: Vote! We’ve opened up a poll for you to voice your opinion on who should win the Binary Battle. We’ll take the aggregate total decided by the public and add that to the judges’ votes to determine the overall winner and runner-up. You’ll have until 11:59 PM Pacific time on Monday, November 28th, 2011 to get your vote in.

Over the past six weeks, PLoS and our friends at Mendeley have been hard at work reviewing all the fantastic apps submitted to the PLoS/Mendeley Binary Battle. We’re pleased to announce the finalists, honorable mentions, and our PLoS Picks. Stay tuned for our announcement of the winners on November 30, 2011!

Finalists (in alphabetical order)

• Collabgraph
• Droideley
• KLEENK
• openSNP
• PaperCritic
• PLoS Impact Explorer
• ReaderMeter
• rOpenSci
• ScienceCard
• TiNYARM
• Total-Impact

Honorable Mentions

• Mendeley Comparison Grid
• Homepage reSearcher
• Vyzkumap

PLoS Picks

Some of our favorite apps featuring the PLoS APIs:

• PLoS Impact Explorer: Developed by Euan Adie, Product Manager at the Macmillan-funded startup, Digital Science, the PLoS Impact Explorer app is an extension of Adie’s Altmetric service, which tracks and scores academic output (scientific articles and datasets) based on the mentions it has received in the press, on reference manager websites, on social media websites, and in literature reviews. This app features a clean, intuitive interface and nicely integrates the PLoS Search API, Mendeley reader counts, and Altmetric’s scores for academic output.
• ScienceCard: PLoS Blogger, Martin Fenner, has created a deceptively simple and very useful app that collects and cleanly displays altmetric and citation information for authors’ published articles (including information pulled from the PLoS ALM API). Registering for ScienceCard is a breeze—in five minutes, you can create an easy, automatically-updated webpage to which can link, use as a reference when collecting altmetric information on your publications, or integrate into your own webpage or webservice using the ScienceCard API. The only downside to this app is that two of the services it incorporates—Altmetric and CrossRef—don’t allow you to click-through to find out more about the numbers displayed on your ScienceCard.
• Total-Impact: Total-Impact fulfills an unmet need for how researchers can collect and display a variety of altmetrics in one place. The app’s contributors (including PLoS authors Heather Piwowar and Egon Willighagen, plus Jason Priem, Cristhian Daniel Parra Trepowski, Paul Groth, Mark Hahnel, and Dario Taraborelli) admit that Total-Impact is a work in progress, as they are managing from 1-20+ different metrics (i.e., citations, downloads, Mendeley readers, unique IP views, etc) for a wide range of academic output (i.e., peer reviewed articles, Slideshare decks, Dryad datasets, etc). Major kudos to the Total-Impact team for taking on this challenging project, and for employing the PLoS ALM API so well!

What next?

The list of finalists will now be reviewed by a panel of influential judges from technology, media and science. Stay tuned for our announcement of the Binary Battle winners on November 30, 2011!

Just eight days after announcing our call for App ideas, we received over 70 top-rate suggestions for scientific and medical apps from our community. Many addressed issues already important to PLoS—post-publication peer review and contextualizing and filtering research for a variety of disciplines. Others submitted ideas that were just plain cool but outside of the scope of the Binary Battle competition.

Now we are passing these ideas along to members of the developer community, who have the coding skills to bring them to life.

Below, we have broken these ideas into two groups:

• Ideas that can use the PLoS or Mendeley APIs and can be entered into the Binary Battle competition
• Cool ideas that don’t use the PLoS or Mendeley APIs (and are therefore outside of the scope of this competition) but you might want to tinker with anyway.

Selected Binary Battle-eligible ideas include:

• An app for displaying the impact of diverse research outputs on your CV or website. For example, how many blogs have written about your paper, how often have your datasets been mentioned in scientific lit, etc. An existing app that does just that, called Total Impact but it needs to be taken from prototype to full-fledged app. More info here and here. Suggested by Heather Piwowar: hpiwowar(at)gmail(dot)com or total-impact(at)googlegroups(dot)com
• Create an easily embeddable, dynamically-updating list of PLoS or Mendeley papers from a particular lab or institution that researchers can put on their websites. Suggested by Sébastien M. Crouze:  seb(dot)crouzet(at)gmail(dot)com
• From a bunch of papers, recursively extract all the references they contain and establish a ranking of the most cited papers. It will help to found “must read” papers from a certain website, subject area, author(s), or institutions. Suggested by anonymous.
• Search papers in Mendeley or PLoS based on geography or genes. Suggested by Sjurdur Hammer:  sjurdur(at)hotmail(dot)com and anonymous, respectively
• A tool that will automatically export illustrations and figures (as well as their attributions and CC licenses) from PLoS papers to the Wikimedia Commons. Suggested by anonymous.
• More ideas here

Other cool ideas

• A searchable directory that could collate grant/funding opportunities from across all Federal, State and Foundation entities that are currently silo-ed into individual, closed databases on individual websites. This master databank should then be sortable by field, interest area, investigators (e.g. young investigators, tenure-track faculty, postdoc, etc.), funding amount, etc. Suggested by Llewellyn Cox, PhD:  llewellc(at)usc(dot)edu
• A citizen science measurement app (like NYC Cricket Crawl) via GPS, photo, video, audio recording that sends data in standardized format. Suggested by mik3cap.
• An app for identifying bat species from the sounds they make. You would hold up the smartphone and it would record a sound and then give you a species identification on the phone. Suggested by Dr. Kate Jones: kate(dot)jones(at)ioz(dot)ac(dot)uk
• An educational App which finds the most recent common ancestor between any two species on the planet. Suggested by aulridgejr(at)gmail(dot)com
• More ideas here

To sign up to develop an idea or request an API key from PLoS or Mendeley, fill out this form. We encourage you to work with other devs who share an interest in the idea you choose, and also to contact the scientist who conceived of the idea, should you seek more input or wish to invite them to collaborate.

Finished apps for the Binary Battle competition must be received by September 30^th. Tim O’Reilly looks forward to seeing your creations – happy coding!

Have a great idea for a scientific app but lack the coding skills to develop it? We’d like to hear it!

Submit your app idea by August 10^th (12pm PDT) and we’ll present it to the developer community, who have the skills to make your dream app a reality. Ten (10) randomly selected winners will receive a PLoS t-shirt (Terms and Conditions apply).

Apps will be created by mining PLoS and Mendeley APIs and will have the potential to make your life easier and science more open.  Here are just a few of the possibilities:

• Mine PLoS articles for statistically relevant words or phrases using the Solr API
• See how many people are reading your papers and how you compare to other researchers on Mendeley with ReaderMeter
• Determine the top papers read by researchers in particular subject areas in both  Mendeley and the PLoS journal family

How To Submit Your App Idea:

• Complete the form at the Binary Battle App Idea Submission site [UPDATE: Now closed!] OR
• Tweet your idea with the hashtag “#binarybattle” OR 
• Leave a comment on this blog post with your idea and an email address

If you’re a developer, you may wish to enter your completed app into the Binary Battle by September 30th, 2011.

By opening up our content and data through this API, we hope to encourage the development of more tools that will improve the way PLoS users discover and interact with our content, as well as their own.

The new Search API gives developers access to rich data that can be flexibly integrated into applications and websites. It allows PLoS content to be queried using any of the fields in the PLoS Search Engine.

There are a number of different ways we can imagine developers using the Search API. To get your creative juices flowing, here are some examples of widgets we have built:

• Default Search
• Author Search
• Title Search
• Subject Search
• Abstract Search

Here’s what Richard Cave, Director of IT at PLoS said about the PLoS API, “We are pleased to be able to allow developers to leverage PLoS content and data to improve their own web offerings.”

To get started, developers need to obtain a key (and all comers will receive one). We look forward to seeing your new apps, and please watch out for an exciting competition announcement in the near future.