Binary Battle App Ideas

Total-Impact Tool for Displaying Impact of Diverse Research Outputs

The idea

An app for displaying the impact of diverse research outputs.  For example, how many blog posts have been written about your papers?  How many times have your presentation slides been viewed and downloaded?  How many times have your datasets been mentioned in the scientific literature?  We envision a web app, currently dubbed Total-Impact that takes a list of research artifact identifiers (DOIs, accession numbers, urls) and scours the internet for metrics of impact through open APIs and permitted web scraping.  The results are displayed at a static URL that can be tweeted, included on a CV, etc.  Described in more detail here:  http://beyond-impact.org/?p=185 

 

We have a working prototype of this system here:  http://total-impact.org, with open source at https://github.com/mhahnel/Total-Impact.  However, we lack the technical expertise and the time to make this app production-ready.  It needs to be able to handle a load and deal correctly with API limitations.  It needs to be prettier and more user friendly.  It should play well on mobile devices.  It no doubt needs better error handling.  There are oodles of more metrics that could be collected.  All the things that would help it be truly useful and usable. 

 

The idea and initial prototype of the system came out of the recent Beyond Impact workshop. The team who has been working on it would love for someone else to pick up the idea and run with it!  We'd like remain involved with the vision, if that is helpful. 

 

Contact us if you want more info???  Or, since the code is open, feel free to run with it as you see fit :) 

 

We think this would be a great contender for the Binary Battle and would be happy to help promote it (twitter, blog posts, etc) for that.  And just in general, because we want to use it ourselves (see commitment in http://researchremix.wordpress.com/2011/08/04/bioscience/). 

 

We also think further development funding for app might be possible through initiatives like the Digital Science Catalyst Prize, and would be happy to help with such submissions.  We just lack the time and expertise to take this project to the next level... we hope someone else will.

How it will make scientists' lives easier or science more open

We think this app is key in moving beyond the impact factor as the key metric for evaluating research articles, and beyond research articles as the only form of valued scientific output.  It would empower scientists to include more diverse products and assessments on their CVs, thereby facilitating a grass-roots movement toward broader-based assessment.

Tech specs

Data sources: Mendeley, PLoS Article Level Metrics, PLoS Search, CrossRef, NCBI Entrez for PubMed Central, SlideShare, DataCite, Dryad, Probably Wikipedia, Ideally blog usage stats, Institutional Repositories, The rest of the web, wherever and however there are metrics of use around scientific artifacts....

Platform(s): web app, including mobile

Languages: PHP, couchdb, some python

Suggested by: Heather Piwowar: total-impact(at)googlegroups.com // hpiwowar(at)gmail.com

Mendeley for iPad – iAnnotate integration

The idea

Mendeley for iPad integrated with iAnnotate! iAnnotate is great for reading and annotating PDFs.

How it will make scientists' lives easier or science more open

Will make it possible to read papers when traveling and away from the main computer.

Tech specs

Platform(s): iOS

Suggested by: Anonymous

PLoS App for Android Devices

The idea

Make PLoS articles readable/searchable/shareable via an app for Android phones and tablets.

Suggested by: Anonymous

Citation Summarization

The idea

Given a paper, extract the content of the sentences where it is cited. The idea is then to create automatically a summary from this. 

 

Example: Paper A is cited like that in paper B and C 

Paper B: "the bibliography software Mendeley is great (PaperA, 2010)" 

Paper C: "Mendeley has been show to improve the productivity of scientists (PaperA, 2010)" 

 

Then the synthesis for the PaperA should look something like:  

PaperA: Mendeley is great and improves the productivity of scientists. 

 

This is a toy example but I'm sure that fancy semantic extraction could allow to get very good results. 

 

This is important because papers are not always cited for what the author intended initially. Some papers can become important for other reason, and this information is only known by people with experience, it is sometimes hard to figure out. It can also highlight the fact that some papers are cited for negative reason (example of a bad method, etc). It would be very useful for people entering a new field.

How it will make scientists' lives easier or science more open

It will add a huge qualitative value to the simplistic "nb of citation" metric. And also constitutes a good entry to papers from a field where are not expert in.

Tech specs

Data sources: Mendeley, PLoS, Google Scholar

Platform(s): Online

Suggested by: Sébastien M. Crouzet: seb.crouzet(at)gmail.com

Exporting Publication List for Labs or Institutions

The idea

Lab list of publications export. It should be easy from the "My publication" section from Mendeley to publish a list of all the publications of an individual/lab on a web page. There is a "way" to do that with a Mendeley badge right now but it could use improvement. 90% of the labs are still managing their publication page manually, there is a huge demand on a simple way to do that and Mendeley (and the PLoS Solr API) has everything to do that.

How it will make scientists' lives easier or science more open

The life of scientists will be easier because it does something automatically that they have to do by hand before. Science will be more open if this list can be followed (for example through RSS), then you can even think that journals might become obsolete.

Tech specs

Data sources: Mendeley, PLoS, Google Scholar

Platform(s): Online

Suggested by: Sébastien M. Crouzet: seb.crouzet(at)gmail.com

Extracting Citations to Find "Most Important" Papers in Certain Domains

The idea

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 domain [ed. note: citations do not equal "most read," but they can indicate an influential paper].

Tech specs

Data sources: Mendeley, PLoS

Suggested by: Anonymous

Suggesting Mendeley Contacts Based on Publications

The idea

An app that suggests new friends based on your publications and library, such as; 

-The Mendeley users that you've cited their papers in your publications. 

-Mendeley users that have cited your work. 

-Mendeley users which has the similar papers in their library. OR reviewers based on publications

How it will make scientists' lives easier or science more open

Mainly networking with people working similar topics with you

Tech specs

Data sources: Mendeley library. Also the author names from the references should be fetched

Suggested by: Ozan: ozikeysan(at)gmail.com

BLAST App for Internal Files

The idea

BLAST App for iPhone/iPad - against genbank but also internal files. BLAST n/x/p and export into a textile which can be used further.

How it will make scientists' lives easier or science more open

Blast from wherever you are

Tech specs

Data sources: nuecleotide AS sequences - NCBI + internally stored sequence files (transcriptome contigs)

Platforms: iOS

Suggested by: evo_devo(at)mac.com

Citation Data Visualization App

The idea

My idea for the app is that for a given list of scientific papers, an app should show the common citations. Papers can be shown as networks with each node representing a paper and a directed edge from node A to node B, if A cites B. The size of node (paper) may reflect the number of citations  

a) made by the papers in the given list. 

b) made by the papers in the given list and papers cited by those 

c) by impact factor

How it will make scientists' lives easier or science more open

It will help scientist to find out what one should read next.

Suggested by: sulav_duwal(at)hotmail.com

Suggesting Mendeley Contacts Based on Publications (Part 2)

The idea

Scientific paper recommender and "most similar user" social networking finder: If you have paper X in your library, then you will probably also like paper Y.  A distance metric between individual users can be constructed based features from the article titles, authors, and tokens from the keywords in the abstracts.

How it will make scientists' lives easier or science more open

It will help keep me more in the loop of papers relevant to my research, and find other people who are interested in the same topics that I like.

Tech specs

Data sources: Mendeley API, pubmed, other publicly available databases.

Platform: Online app with plugin to Mendeley

Suggested languages: mysql, R, ruby on rails

Suggested by: Tiffany Chen:  tjchen(at)cs.stanford.edu

Reference Management Software as Manuscript Writing Support System

The idea

Every reference management software has a potential to become a personalized manuscript writing support system with some simple functions as I described in http://www.mendeley.com/c/3685419131/p/564621/todoroki-2010-bibtex-based-manuscript-writing-support-system-for-researchers/ 

Mendeley is not an exception. I'm already enjoying this system with BibTeX and hope the idea prevails further.   Then, I will have a chance to switch from BibTeX to Mendeley.

Suggested by: Shin-ichi TODOROKI: TODOROKI.Shin-ichi(at)nims.go.jp

A "Hot or Not" for Scientific Ideas/Articles

The idea

Rating-Application - for this and that! 

 

Guess you know all these rating-pages on the web for rating people. You give a number of 10 if you like her or 1 if completely not. Once many people have clicked you, you get a rating.  

 

However: given a number is very uncertain. And the process is very slow. You need lots of clicks to get a reliable rating.  

On the other hand: if you have to decide between two things (pictures), your choice gets more reliable. Within a few comparisons with other things (pictures), you get a reasonable number. Like in chess player ratings, for example.  

 

I think there is a need for quick and reliable ratings in many areas, not only just pictures, especially in areas where subjectivity is predominant. Not just facts, just feelings. Feelings are difficult to reduce to merely a number.  

 

You could use this app for many areas:  

- comparing (comparable) pictures 

- comparing music 

- comparing ideas 

- comparing wisdoms 

- etc.  

 

The app should be easy to implement to just compare things directly side by side in any given community. E.g. as a photographer I want to know whether my picture is really as good in the eyes of others as I think. With the app a get a rating which is way better (more reliable) than any benevolent comment on a photo-site.  

 

You could even use this scientifically to test for e.g. detecting the ability to hear the difference in the mp3-coding of music: which compression can be detected as being superior? Is mp3 128 kbps really the same for your ear as 192 kbps etc.? Can subjective evaluation enhance objective evaluation in different areas of life? 

 

The app should simply present two (or more where appropriate) things to compare. By just clicking on one item the app does the calculation (e.g. like for chess players (algorithm by M. Glickman, Boston)) and present the current result in a meaningful manner to the user.  

 

While "subjective" is subjective, there seems to be a contradiction in this approach. However, subjectivity leads sometimes to false conclusions. Here the app comes in giving as some kind of useful objective feedback.

[Ed note: we believe that a similar system, when applied to papers in certain subject areas, could be a useful alt-metric.]

How it will make scientists' lives easier or science more open

Objective evaluations in subjective areas.

Tech specs

Data sources: Web-Input -> SQL-DB -> Output

Platform(s): Online

Suggested by: Reinhold Gellner: gellner(at)uni-muenster.de

Location-based Search

The idea

I would like to be able to search available literature based on geography. For example I would highlighting a place on the planet to find out any scientific literature to do with pollutants in this region, or maybe somebody would like to find out about spiders in a specific region. This would be a long term goal, and would obviously require for literature to somehow be geo-tagged accurately, but it would be a super useful tool in literature search. Likewise it could be cool if people search on Mendeley could be geographically limited, so it would be easier to find local researchers, or researchers in a location, where you intend to do future field work.

How it will make scientists' lives easier or science more open

I think this would improve the connectivity of the scientific community significantly, and would make literature search much more exciting.

Suggested by: Sjurdur Hammer: sjurdur(at)hotmail.com

Auto-upload Figures and Illustrations from PLoS Papers to Wikimedia Commons

The idea

Open access papers are usually published under a free license like CC-BY-SA. Therefore, the illustrations and images in these papers can be reused elsewhere as long as the conditions of the license are met. Some of these images are useful at Wikipedia, which makes it attractive to upload them at Wikimedia Commons. 

 

The app I would like to propose eases the copying of images from journal sites like PLoS to Wikimedia Commons. The app should automatically copy the license conditions and use the image description from the paper.  Nevertheless, the latter should be offered for modification to the person using the app.

Suggested by: anonymous

GitHub for Lab Work

The idea

I desperately need an app for the lab. Something with a synchronizable notebook, protocol organizer, sample storing database and, more importantly, that can link experiments to papers filed with Mendeley and the possibility to create a community (public or private) to share and comment experiments with.

Tech specs

Platform(s): PC, Mac and, very important, android and iOS

Data sources: Mendeley and desktop app

Suggested by: Luis: querolus(at)gmail.com

Gene-based Search

The idea

Find papers on a specific gene. Yes, NCBI already does this but what about on Mendeley/PLoS?

Suggested by: anonymous

Wikipedia Editor

The idea

App to help authors write/edit Wikipedia pages in order to better insert references from Mendeley and PLoS. Develop ways to introduce photos, write information in a WYSIWYG fashion.

Suggested by: anonymous

Headache-mapping App

The idea

Headaches are a global burden: http://onlinelibrary.wiley.com/doi/10.1111/j.1468-2982.2007.01288.x/full 

"headache" appears in thousands of tweets everyday: http://trendistic.indextank.com/headache/_30-days

 

There are quite a few headache-diary-apps out there but - as far as I see - none of them tracks headaches geographically so that something like a "headachemap" would be possible: where in the world do how many people suffer right now from a headache (and have it entered into the app)? 

 

So I propose: build a multiplatform app to enter basic data about the headache its user has, add gps-data to it and collect this information in a database that feeds a worldwide map of headaches occurring. possibly show the resulting, over time changing map(s) similar to weather charts. Add headache-relevant papers where possible and adequate. publish the gps-headache-data under a CC-license, but think of a way to keep the privacy of participants (maybe add a "blurring-factor" to the original location data of the headache). 

 

I did put a few sketches about this idea in German here:  

http://io3.ch/doku.php?id=kopfwehkarte

How it will make scientists' lives easier or science more open

It might make possible a lot of new innovative research with the collected data on questions like temporal associations between weather and headache etc. See e.g. http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0014612

Tech specs

Data sources: data entered by its users, plos/Mendeley where adequate, map servers like Google and / or openstreetmap, weather data

Platform(s): iOS, android etc.

Language(s): c++, html5, javascript

Suggested by Patrik Tschudin: patsch(at)gmail.com

Mind Mapping Lit Review Software

The idea

Mind mapping software for literature review (showing the relationships between references, follow on research, cross referencing etc). Qiqqa has something like this, but it's not there yet.

How it will make scientists' lives easier or science more open

It makes it easier to catch up on the flow of research in a more logical way

Tech specs

Data sources: It could be an add-on for Mendeley

Platform(s): Windows, Linux, Mac

Institutional Repository Sync

The idea

Not such much an app as an add-on... I'd like to see someone build an open source tool that would bring personal archiving capability to Mendeley and PLoS.  Essentially, it would create a link with the user's IR so that they could periodically archive materials while in the flow of their research.  This tool could be adapted by different Universities to work with their IR, and would encourage even broader use of Mendeley (and perhaps more cross-institutional research sharing).

How it will make scientists' lives easier or science more open

Much more open, as it would encourage researchers to archive their works and other materials in IRs

Tech specs

Data sources: Mendeley or PLoS data, user's desktop data, local IR data

Suggested by: Ellysa Cahoy: ellysa(at)psu.edu

CiTO Support for Mendeley and PLoS

The idea

Full support for CiTO. For each article in my library (with enough citations) I want to be able to see something like a pie chart the number of papers that use data, use results from that paper, and how many papers cite that paper merely as reference, or even disagree with it. Such a pie chart is just the start. For each category I also want to be able to see a Wordle for the keywords or abstracts for those papers. As such, I get a much richer view of the impact of that paper, also making it possible to find relevant new literature. 

 

So, the GUI of the app should consist of basically three elements: 1. the pie chart, 2. clicking on a pie chart gives Wordles of keywords, 3. clicking a keyword give the citing papers with that keyword.

 

(1. credit should go to David, of course, who actually implemented CiTO) CiteULike already has CiTO support, and content there may be use as initial support. The App, of course, would make it damn easy for users to add such typing, and text mining way provide initial types as suggestion to the user, showing the sentence where that paper is cited in the citing paper.

How it will make scientists' lives easier or science more open

Because it makes it clearer how the community thinks of a paper.

Suggested by: egon.willighagen(at)gmail.com

Mind Mapping Lit Review Software (Part 2)

The idea

A scientific note-taking / sketching / mind-mapping / brainstorming tool that has access to my Mendeley library/PLoS publications so that I can 1) add citations to notes and sketches as well as 2) make general notes / sketches about a folder in Mendeley. Should be able to search for references as can be done with the word plugin. 

Clicking on a reference in this app should allow you to see basic Mendeley metadata / abstract / notes within the app as well as provide an option to go to that citation in Mendeley desktop. 

 

Note: I have just done an internet search and discovered whilst filling out this form a program called Sciplore mind-mapping - which seems to have some components of what I am proposing (the ability to add Mendeley references via a synchronized bibtex database). http://sciplore.org/software/sciplore_mindmapping/ 

However, I have not yet tried out this program and I am suggesting it would be better to have tighter and more dynamic (back-and-forth) interaction with Mendeley via Mendeley APIs. 

 

Having not yet tried SciPlore, I don't know if it would be better to do this by building on SciPlore (which seems open source) or in a totally new app.

How it will make scientists' lives easier or science more open

It will join together aspects of the research process that are currently disjointed: namely reading / reference management with idea generation/planning.

Tech specs

Data sources: Local Mendeley desktop on my PC.

Platform(s): Any platform that Mendeley runs on

Suggested by: Omar Mian; o.mian(at)ucl.ac.uk

Funding Suggestions Based on Mendeley Library

The idea

A service/app that provides me with recommendations for funding calls / grants / fellowships / scholarships as well as upcoming conferences based on the contents of my Mendeley library.

 

This could be a desktop app, but I envisage this would be more useful as a web service which sends me periodic emails with recommendations. Ideally, I would like to be able to select which groups in my Mendeley library the recommendations are based on.

How it will make scientists' lives easier or science more open

Would allow me to spend less time searching for suitable grants / conferences

Tech specs

Data sources: Mendeley Libraries of individual users, various funding websites 

Platform(s): Any platform that Mendeley runs on, Web

Suggested by: Omar Mian; o.mian(at)ucl.ac.uk

Seminar/Meeting Suggestions Based on Mendeley Library or PLoS Publications

The idea

Seminar alert. Database where everybody can post their seminars/meetings linked to your personal literature database. So if you read papers of author x or have notified that you are interested in work of author x, the app will notify you if this person will give a seminar in your neighborhood or on a conference. You can choose what you neighborhood means (i.e. same state/country/continent/world). 

How it will make scientists' lives easier or science more open

This app would be helpful for people who organize meetings/seminars but also for people who want to listen to or get in contact with certain people.

Suggested by: w.bitter(at)vumc.nl

Facebook Tool that Posts Mendeley and PLoS Papers

The idea

Post an article information containing a link to the article on your Facebook wall everyday, which is related to your "interest" on your Facebook profile.

How it will make scientists' lives easier or science more open

This app will let ordinary people more interested into sciences. They will have more opportunities to read/see/browse research articles.

Tech specs

Data sources: Mendeley, PLoS

Platform(s): Facebook

Suggested by: Kanako: kany1120(at)myopenarchive.org

Social Reference Manager with Citation Info and Ratings Integration

The idea

I would like very much an app allowing me to (in sequence): 

1) insert data about a specific scientific publication (article or book) via doi or isbn 

2) rapidly see (in just one screen) which articles or books have cited the selected publication, with if possible the citing sentences 

3) rapidly see (in just one screen) comments, criticisms and any other kind of feedback about the publication, published with a nickname or anonymously 

4) share the publication's data and/or my comments about it with a group of contacts and/or publicly  

5) have a private part where I can add personal notes and manage my references, that can be used offline and standalone 

6) allow the user to "follow" a certain publication and to be informed as soon as new comments or criticisms are posted (for instance by RSS feed). 

 

This app would join the good aspects of Mendeley, CiteULike and Zotero, enhancing the participatory aspect and the linkages with other publications (so allowing the researcher to discover new texts).

How it will make scientists' lives easier or science more open

It would make easier to discover new content and ideas and to get to know people with the same research interests as mine.

Tech specs

Data sources: Google Scholar data search, Mendeley and CiteULike databases

Platform(s): I hope that it will be able to run on Windows and Macintosh OS. I think that it could be interesting to realize also non standalone versions to be integrated to Mendeley, CiteULike and Zotero online platforms.

Suggested by: Paola Rattu paola.rattu(at)unil.ch

Blogpost/Website Impact Measurement Tool

The idea

An app that can crawl for + compile list of blogposts/MSM articles/websites that cite or link to a particular journal article!

Suggested by: younglandis

Scientific Myth Dispeller App

The idea

As a layperson science fan/supporter, I'd love to see an app that presents common myths…that misrepresent true scientific consensus, with plain language explanations why said myths are false, and links to supporting articles in Mendeley/PLoS.

Suggested by: denbutsu2

Better Figure Searches

The idea

App idea: restrict text search to figure legends for papers available in Mendeley. Results should include link to published figure online + email of corresponding author for permission request + links ref. publications in legend.

Suggested by: LourencoZe

Dictionary for Scientific Terms Used in PLoS Articles

The idea

I have this function in my kindle app where you click on a word (or touch in the case of smart phones and iPads and the like) and it opens up a dictionary function. Would help immensely with the scientific articles I read. I mean I'm no dummy but I'm also not a walking dictionary. So maybe an app that adds that function to my (android) phone/ iPad.

Suggested by: Daniel Williams

Mind Mapper for Scientific Articles

The idea

A mind mapper which lets me construct argumentation patterns by connecting nodes with arrows of kind e.g. 'contradiction', 'solution', 'conclusion' or similar. The nodes would be linked to the mendeley article database. Click on node => article shown. It might make sense to store whole node patterns within nodes of higher level. A mind mapper of similar kind is Compendium.

How it makes science more open or scientists' lives easier

Gives overview on argument pattern.

Tech specs

Data sources: mendeley data base, I think it should be a plugin.

Platforms: win, linux

Suggested by: Anonymous

RSS Feed Subject Disambiguation App

The idea

I find it annoying that, because I have signed up for PLoS ONE RSS feeds under several headings, if a paper falls under more than one heading I get the notification more than once. So: an app for PLoS ONE that collates RSS results from several headings into a single stream with no duplicated hits.

Suggested by: j.bundy@imperial.ac.uk