The app ideas below that we received as part of the Binary Battle Call for Ideas don't exactly fit within the scope of the Binary Battle competition but are nonetheless worthy of consideration, if you're looking to build a cool scientific app.
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.
Collation of opportunity announcements from across all sources and sortable by type, amount, interest area, target investigators, etc. would greatly increase the efficiency of investigators in finding appropriate sources of funding to apply for, allowing them to spend time more effectively on creating the actual applications and executing their research programs.
Platforms: desktop, tablet, mobile
Suggested by: Llewellyn Cox, PhD: llewellc(at)usc.edu
Can quickly search my own paper library
Data sources: any RIS, Endnote, etc. bibliographic files
Platforms: iPhone, iPad
Suggested by: corey.bradshaw(at)adelaide.edu.au
A lab internal twitter.
Labs continue to rely a lot on mailing list for most of communications. 90% of this communications would be more appropriate in a twitter-like form: "conference in room 200 at 2pm" "look at this paper this is great http:apaper.pdf" "how to make a matrix sparse in matlab?"
The #keyword is obviously nice in this context. The (at)someone would be very useful because you could for example send a paper to the member of your lab you would have mail it before, but the other can also look at it if they are interested.
Improve intra-lab communication.
Platforms: It can be independent or include into Mendeley
Suggested by: Sébastien M. Crouzet - seb.crouzet(at)gmail.com
A small app that send you a message that the Space Station is about to pass overhead, and from what direction.
Put a smile on my face
Suggested by B. Burgess, help(at)pscfg.com
An app that gives you access to a dynamic, zoomable 3 dimensional TREE OF LIFE. The first few thousand species come with the app, all the others get added over time by users of the app (and accompanying website) a la Wikipedia, with annual awards for the users who add the most (accurate) info.
This hasn't been done... yet. It would be something that scientists and non-scientists can compete in.
Data sources: Wikipedia, user generated content. You'd need to make a branching folder-like system for the backend (to add to the tree) and an all singing, all dancing graphical tree for the front end.
Platforms: Smart phones, all net browsers
Languages: C++, java
Suggested by: Graham Hughes graham(at)theodysseyexpedition.com
Leaf area index (LAI) from forests, fruit trees or grapevines is essential for Functional Plant Models, to scale up leaf based measurements or to monitor canopy vigor and structure. At the moment, this can be done using allometry (destructive methods, this is stripping canopies and scanning every leaf), which is time consuming, unpractical and expensive. The other method is indirectly using expensive instrumentation such as ceptometers, Licor 2000/2200, etc, which are based in light scattering and gap analysis. A digital cover photography method has been validated for forests and grapevines (Dr Sigfredo Fuentes) and can be incorporated as an app that can be run in any smart-phone, iPad, iPhone with in-built digital cameras. An automated image acquisition and analysis has been developed in MATLAB. This could be a great idea for an app and I have seen a number of people and scientists around the world that already have asked me and are using the MATLAB code for their research.
If the hardware containing this potential app have GPS capabilities, maps of the distribution of parameters obtained can be obtained too.
More info: Functional Plant Biology (2008), Volume 35 Issue 9/10, pages 1071-1079
This will contribute greatly to modeling and monitoring of canopy architectural characteristics
Data sources: Digital images obtained from the hardware in which the app will be installed.
Platforms: Android, iPads, iPhones
Languages: C++, MATLAB
Suggested by Dr Sigfredo Fuentes (sigfredo.fuentes(at)adelaide.edu.au)
Make an app with functionality similar to the Khanacademys practice-section, but for physics.
The idea is to "gamify" science-learning, by having exercises with points awarded for right answers, achievements like "500 points for 10 correct answers in a row" and so on, learning is fun, and motivating.
The knowledge-map approach is breaks even complex knowledge up into small pieces, and lets you practice one at a time, until you master it all.
It will teach science to new groups
Data sources: integrating the app with Khanacademy would be awesome. (the code for that is already open-source)
Platforms: html5 for maximum availability
Suggested by Eivind, eivindorama(at)gmail.com
My idea goes along the lines of chemistry. I would like to see an app that includes molar computations, compounds that can be made through 3d experiences and balancing equations. And of course a periodic table that's interactive showing densities, specific heat, etc.
It provides a quick reference
Suggested by: Eric Markham: 1karatekidcapecoral(at)embarqmail.com
Identification of plants, animals or other natural features.
There are lots of identification books for plants, including all the identification keys like color of the blossom, number of stamen etc. But when you are on a walk or excursion you only can use the features of the plant that are currently visible (maybe there is no blossom, but you could tell the form of the plant stem or the size of the seed. I would like to enter all identification keys that are available and get a list of possible items (plants in this case) that match the keys. I then could view the pictures and find out what plant it is.
Faster and better identification
Data sources: Use of existing identification literature
Platforms: Mobile devices
Suggested by: Gerhard Hofmann, gerhard(at)blaukasten.de
Signaling pathway maps
Easy access to signaling pathways wherever I want
Platforms: iPhone, Windows Phone 7
Suggested by: ceang(at)stanford.edu
For the growing field of social network analysis, especially in the political sciences, it would be very helpful to have a social network analysis tool explicit for Mac! There are some great apps out there like visone or UCInet, but those are old fashioned and mostly not for Mac (despite the Java-based visone). But most of them lack a good User Experience and Usability. Such would be a great app!
Faster and more comfortable analysis of social networks.
Data sources: data from simple excel sheets to advanced data sets of the common network analysis tools like visone, UCInet, pajek etc.
Platforms: Mac OS X
Languages: Cocoa - Mac Stuff
Suggested by Timo Burmeister, timo.burmeister(at)gmail.com
I often try to think of a single gel capable of separating and/or visualizing the DNA, RNA as well as the protein content of cells. It will be like a crude cell extract will be run on a gel Agarose, Polyacrylamide or the mixture of the two which will be cast in a way so that the different molecules (having different charge, size and other properties) will moce at different speeds in an externally applied electric field. This will save a lot of time, money, efforts and reagents to separate the DNA, RNA and proteins of a cell suspension. Furthermore, we always need to deactivate other molecules when extracting one. For example we have to add proteinase when extracting nucleic acids which destroys the proteins in the cells. We also add DNA out (which destroys DNA) while we extract RNA. So we only get only one type of molecule from a cell suspension. Using my idea, we can separate all the three types of molecules from a single cell suspension. The pore size, Ph, voltage and the buffer needs to be standardized for this technique.
It will help the scientist to do more work on a small amount of sample. It will also reduce the cost of many experiments by more than 50%. Also the time taken to separate the different types of molecules will be reduced three times. Reagents will be saved and the method will be relatively easy and far less cumbersome.
Suggested by: Muneeb Faiq: muneeb1983(at)yahoo.co.in
An educational App which finds the most recent common ancestor between any two species on the planet. For example: The most recent common ancestor between slugs and human beings. The App could demonstrate the stages of evolution in reverse, showing how slugs and humans evolved over time in side-by-side panels. Ideally, the App would also allow the user to start with any one species of animal and then trace it backward through enormous generations of time to see what was its most direct common ancestor, along with cousin species, and the era in which they lived.
Call it "The Genealogy of Species". Or...something better, I'm sure you lads and ladies are far cleverer than I am.
This App will provide a visual history of the genealogy of all species (or at least, a lot of species) on this planet. This will help young children and students to more readily comprehend the concept of evolution in a way purely textual information may not be as capable of doing as easily.
Platforms: Linux, Windows, OS X, Android, iOS
Languages: C++, Java, Python
Suggested by aulridgejr(at)gmail.com
An app to decide which markers to use to differentiate specific cell populations. The user would input the cell populations they would like to identify (fibroblasts, neutrophils, myocites, etc) and the app would show markers that differentiate the populations from each other. Potentially, the app could suggest markers that would differentiate all of the populations from other cell types. For example, if the user wanted to differentiate between the different lymphocyte populations, the app would tell the user to use CD45 to eliminate non-lymphocytes, then CD19 to identify B cells, CD3 for T cells, CD11c for dendritic cells, etc. Additionally, this could be reversed so that if the user has a population that they don't know how to characterize, the app can tell them the potential cell types for the given markers.
It will make identifying cell populations in flow cytometry much simpler.
Suggested by: Jackson Eby, jackson.eby(at)epfl.ch
I've been thinking many time I would like to have an application on my iPhone that would give me statistics. A bit like the wolfram app, for example you enter a request like Christians in France and it would give you the percent of Christians living in France and other statistics concerning those two entries (Christians, France)...
It would help me writing
Data sources: Statistics organisms' databases like the INSEE in France for example.
Platforms: Phone, IPad and other smart phones
Suggested by: Morgan Flament morganflame(at)gmail.com
E-Lab-book app. A diary/journal format app that researchers could use to record notes, protocols, tips, images, graphs, and results in a manner that is potentially openly accessible to the internet. This would help avoid duplication of work and provide a more transparent system of research documentation.
Would promote digitalization and easier dissemination of daily-used tips and tricks used by scientists.
Suggested by: Pooja Rao 1985.pooja(at)gmail.com
A graphical journey of the universe. From the edge of the universe to the subatomic. Scroll around and click on objects, e.g. stars, to zoom in and get some information about the object. Zoom in further and see the processes involved with snippets of information of what's going on. Into the subatomic showing atoms with revolving electrons. Zoom in further to see the protons and neutrons. Electro magnetic fields etc. The scale could be from the big bang lots of color and energy, to the small, which could be a scroll through the universe and end up at earth, scroll in further to see the subatomic nature of matter. Could do it for biological organisms too, so scroll into an organism and see the genes and DNA and how these interact and create life. Concise info on each level of magnification. Good looking is paramount.
On the journey through the universe you could 'stop off' at places, say a nebula, and see the formation of stars, the dying of stars, the creation of black holes and neutron stars. It would be fantastic, especially if the designers were anal with the level of detail.
It'll make science more open because people will be able to scroll from the very large to the very small in a factual and, most importantly, graphical way
Data sources: Scientific journals. The more data gathered the more detailed the app could be.
Platforms: All graphical platforms
Suggested by: ian_breaker(at)live.co.uk
As a molecular biologist I yearn for an app that is an all-in-one periodic table, amino acid table, nucleotide bases and functional group encyclopedia. A couple of apps exist (i.e. The Chemical Touch) that cover a few of these areas but none do everything.
All the fundamental information for molecular bio/genetics will be accessible in your pocket. No need for the internet, a textbook or posters. It would be fabulous.
Data sources: All of the information for constructing this app is factual and can be found from most university molecular/biochem texts.
Platforms: iPhone, android, touch-based devices
Suggested by: Chris Langley chris.r.langley(at)gmail.com
An App that can import DNA data from all present available genotype/sequence formats and platforms (23andMe, completegenomics, etc), and that could be use as a tool to gather information about the genome in any possible way. For example, just to check a specific genotype from a specific position that just appeared in the news, or the information associated to a specific polymorphism or haplotype.
Add-ons could be implemented to add capabilities.
Data sources: Public Human Genome data and related databases like snpedia.
Platforms: IOS, Android, Symbian
Languages: Java, Perl
Suggested by: David de Lorenzo, david(at)delorenzo.com
Not so much an app idea as a website / service idea: It would be cool if amateur astronomers could agree via a forum or collaboration app or something to all take a picture of, say, Mars, through their telescopes. Their cameras could be connected to their laptops and the images would be sent via their wifi & internet or 3g phones to a server that can combine their images to create a sharper image. As more people submit / update their images the combined image would be updated and people could watch it evolving every few seconds. Much like optical astronomical interferometry where a number of widely distributed Earth-based telescopes act together as a larger telescope.
I think there's something called the drizzle algorithm, which has an sdk (there's also something similar called stacking), and which could be used for combining the images.
Amateurs could combine their powers and have fun! It could help beginners learn how collaboration is a big part of science!
Suggested by: Greg Burke gregtheburke(at)gmail.com
I'd like an app that streamlines archaeological field work. I have a lot of ideas, but I'll try to give the gist. Basically, you would start a "Project," and fill in the relevant information, e.g. State, Site Number, Site Name, GPS coordinates (taken from the phone's GPS), etc.
After "Project" is "Forms." Forms are standardized, so you'd have to pick which type, based on regional National Park Service forms by default (MWAC, SWAC, etc). Maybe different forms and form styles could be added with updates. That could be in the "Project" setup screen.
Finally, you choose a form to fill out (Excavation, Shovel Test, C-14, Human Remains, etc), and each form would have its requisite fields (Excavator Name, Screener Name, Shovel Test Number, Depth, Screen Mesh size, Map Coordinates, GPS Coordinates [again, taken from the phone's GPS] etc), while info from the "Project" would automatically appear in the form. You could have check boxes (Screened? etc) and a "Notes" box. There would be an artifacts section to list artifacts found, with an option to take pictures associated with them. Strata would have fields in order to detail their Munsell colors and soil types. Check the "Mottled?" box, and another Munsell field pops up for the same strata. Optionally, photos could be taken of the excavation, soil, artifact, etc, and tied to the form for reference.
(With regard to soils: (1) Maybe throw in a small button that, when pressed, displays a short guide or flowchart to determining soil type. (2) I know this is would be impossible, due to licensing and variability in camera qualities, but it would be amazing to take a picture of soil and have the app determine the Munsell color - that could be an app all by itself.)
The crowning payoff: All of the forms export to a single Word document, determined by the Form Type (MWAC, SWAC, etc), with empty fields to be filled in at the office, if need be. These could even be sent from each excavator to the principal investigator. The PI could then "Combine Projects" which would compile all of the forms into one collection, ready for export. Most of the time, forms that are filled out during fieldwork become dirty, muddy, sweaty, and crumpled, so more times than not they are rewritten on clean sheets in legible handwriting back in the lab. This app would cut paper consumption and cost in half, as well as increase labor-cost.
I call it "Shovel Bum Pro." I would love to discuss it more. Thank you.
It will streamline the process of paperwork, and keep field notes consistent. Consistency is key when a dozen people are recording data, and it would lead to much better archaeological interpretation.
Suggested by: Dick Powis richard.powis(at)gmail.com
Link the experimental protocols used by different labs on the same technique. Merits and demerits of each can be linked.
It will accelerate the research and broaden the knowledge.
Suggested by: anton ilango : antonilango(at)hotmail.com
…I just want a reference to go from pubmed (or any database) into my text where it can be formatted, reformatted, reordered and just do what its supposed to...I know everyone says they have cite and write, but they don't. Its copy and paste, or cite and crash, or cite and reformat. I think word processors are old fashioned. I don't see why we can't take TinyMCE or other real text editor, and create an online environment that uses DOIs or a mysql database to format references within the text editor using a jquery or something like that. Then you can connect it with Mendeley or other open sources. Also, the references would be accessible to the journal for proper formatting…
Data sources: Pubmed
Suggested by: Greg softwallcave(at)yahoo.ca
An app which allows the user to take photographs of unidentified flora - and identify it. You take a photo, and the plant or flower is identified by way of an algorithm, before you receive an email or text back with info on the plant and a link where you can purchase it. Website linked with further information on birds, gardens and natural habitats as well as indigenous and foreign species. Links to RSPB and Royal Horticultural Society
As well as email links back, the app would be linked to a website with information about related animals/butterflies and habitat, shopping features (buy seeds and plants)
Platforms: I-phone and other internet enabled phones
Suggested by: Kate Vines katevines(at)gmail.com
An arxiv 2.0: an open source journal with inclusion of refereeing process based on volunteers, with an open access to the referees reports (i.e. publicly available reports, comments and replies by anyone), plus possibility to have video deposit for experiments, comments, ...
It will allow both version updates of a paper (as it already exists on arXiv) and more transparency in the referring process. Moreover, the public referees reports might be of help to have several points of view on the dame research topic.
Suggested by: anonymous
A web browser which really displays mathematical expressions.
Actually, for mathematical display on a screen, there is not so much choices: or we use lateX (or any software able to publish some equation, but then it is not in an open format) and then compile a pdf with bad display options (for instance, a lot of physics journals are in two columns formats which totally not adapted to screens), or we can use graphics (as in wikipedia) with the problem that zooming is impossible, and display layout are difficult to configure.
I would like to have a browser able to display easily and beautifully mathematical expressions... but I definitely have no idea on how to do that :-(
It must be as powerful as a latex to pdf conversion is in terms of mixing text and mathematics, but at the same time, easy to reflow and zoom as an html page is.
Of course such a format will be more portable than latex for instance (which requires a complete compilation to be displayed), thus more universal, and will allow external software to share mathematical notes. That would be a really good staff!
Data sources: I know about mathml and other ersatz, but I believe the optimal mathematical display is still to be invented. Maybe the wikipedia latex to graphics converter is an excellent starting point, and maybe svg format would be of help. To me, is seems that vectorial graphics are the cornerstone between text and html display.
Suggested by: godzatswing(at)gmail.com
An app for identifying bat species from the sounds they make. You would hold up the smart phone and it would record a sound and then give you a species' identification on the phone.
This app would open up the nature world to non-specialists and help citizen science projects monitor the natural world more effectively.
Data sources: Reference libraries of bat calls; Identification algorithms for identifying parameters of the calls to species (I have one for Eurasia)
Platforms: iPhone and Android
Suggested by: Dr. Kate Jones kate.jones(at)ioz.ac.uk
Why I cant I just type "50 mM tris-Hcl pH 7.8 using Sigma Trizma" and get an application to write me a buffer or solution recipe
Make it easier to make buffer solutions
Data sources: Pubchem to get molecular weights and pKas and such. Sigma / Fisher/ VWR common chemical supplier websites to get formula weights and such
Suggested by: Hari Jayaram: harijay(at)gmail.com
Universal interface for liquid handling automation robots. Automation in everyday laboratory procedures is seriously hampered by the lack of a universal standard among the three or four laboratory automation providers. It will be great to have a universal human readable/writeable automation standard for liquid handling instrumentation.
Automation allows us to increase the complexity and throughput of experimentation.
Data sources: A lot of liquid handling automation products: Qiagen robot / Tecan Robot/ Hamilton robot/ Formlulatrix Formluator all have custom software to handle simple tasks like serial dilutions , liquid gradients etc. Typically this custom software is rather difficult to use and does not adhere to any usability principles. It will be nice to have a standard csv or tab delimited protocol format that all robots agree to use. And a utility that easily converts protocols between these machines
Suggested by: Hari Jayaram: harijay(at)gmail.com
Some kind of 'name that logical fallacy' app where you enter a phrase and it suggests what it is?
Suggested by: CPoeticLicense
Citizen science measurement app (NYC Cricket Crawl) via GPS, photo, video, audio recording. Sends data in standardized format
Suggested by: mik3cap
I need an app to organize and show sound, video, pictures and other stimuli to do research with autistic children.
Suggested by: luizbfreitas
"Unrealistic suggestion for an app: take a picture of a poo and lets you know its bacterial composition" [Editors note: Why not?]
Suggested by: yowino
App idea: restrict text search to figure legends. Results should include link to published figure online + email of corresponding author for permission request + links ref. publications in legend.
Suggested by: LourencoZe
I’d really love an app that could identify birdsong and frog calls. You could record the sounds, it checks a database, and gives you potential matches. It’d also have a function where you could type in the name of a species, and it plays audio of the call/song. It could have different versions for different regions. The first region, naturally, would be Sydney, Australia.
Suggested by: Margaret Morgan
I'd like a microbiology app that allowed you to search based on species or test results. You could enter E. coli. and find out if it's gram + or -, or you could say you have a gram - cocci and see what it might be. It could also have further information, like pictures of colonies, virulence dangers, discoverer, etc..
Suggested by: NH King
Is there a Richard Dawkins biomorph from The Blind Watchmaker app for the devices you have in mind? Or even a Conway's Game of Life app
Suggested by: halucigenia
Is there already an app that allows you to learn information in a way that stimulates both hemispheres of the brain? It would be handy for people who are predominantly right brained but would like to be able to understand scientific reasoning. Another idea is an app that can measure the strength of your cognitive abilities and tell you what kinds of people/activities would be most interesting for you to engage with. That is, of course, if such apps do not already exist.
Suggested by: roisin.ni.mhorain