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Apr
18

Green Chemistry and Engineering Business Plan Competition – ODDT app

Many things are done out of order, yesterday proved that to me. perhaps one would normally have an idea – develop a business plan, develop product and then develop user guide..not us, lets scramble it a bit…

Yesterday was an all out ODDT day (pronounced oddity)..First up there was the business plan. Last year I had attended the green chemistry and engineering conference which sparked the green solvents app  by Alex Clark. It just so happens that this year they are running a business plan competition. We figured that its worth a try because the ODDT app has a green chemistry component, collecting tweets on this so far and storing green solvent information etc. and of course by exposing green chemistry in an app that makes it pretty useful to influence scientists working on rare and neglected disease drug discovery. Perhaps they can start being green right at the beginning?

Anyway it took far longer than imagined to write the answers to the various business plan components but in our spirit of blogging about our ideas for ODDT right from the outset, here is some of what we submitted. As the proposal is unlikely to be kept confidential, we may as well put some of the more interesting bits out there. I held back the less interesting strategic bits for obvious reasons.

1. Public Summary –

Open Drug Discovery Teams (ODDT) is a free mobile app intended as a research topic aggregator of science data collected from various sources on the internet. It exists to facilitate interdisciplinary teamwork and deliver access to information that is highly relevant and focused on the topic areas of interest. Research topics include areas of chemistry and adjacent molecule-oriented biomedical sciences, with an emphasis on those which are most amenable to open research at present. We have focused on green chemistry as a topic due to its importance for scientists involved in drug discovery of rare and neglected diseases.

Executive Summary

Please fill out the sections below and stay within the suggested word limit. You can also attach a 5 page summary below with the same sections included.

The strategic problem and/or opportunity [300-450 word limit]:

Drug discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. With new mobile computer hardware and software applications, aspects of drug discovery will be done anywhere by potentially anyone, while emerging technologies could be used to reimagine the drug discovery process. Tools for drug discovery collaboration predominantly revolve around desktop computer applications though we believe that we will see a natural evolution toward the use of mobile apps in the drug discovery laboratory. We are increasingly seeing a shift to more companies, institutes and researchers openly sharing data predominantly in the neglected disease space. Alongside this there are increasing efforts by researchers to publish in open access journals and release data into open or free databases. How can we possibly connect all of this data and impact research? We believe scientific mobile apps may have a role to play in collaboration and lead us to develop an app called Open Drug Discovery Teams (ODDT) for the sharing of scientific data initially focused on neglected and rare disease drug discovery. Researchers working on these diseases are generally spread throughout the globe and in developing countries. Many of the rare diseases attract little funding and therefore less research, so how can we draw attention to them? Importantly, pharmaceutical research develops molecules that require multiple complex synthetic steps to produce, whether for major diseases like cardiovascular disease or rare and neglected diseases. There is high attrition in drug discovery, so many compounds will need to be made but only a very small fraction will make it into the clinic and, far less, into the marketplace. It is therefore important to design a green process as early as possible when the cost is lower and the quantities of chemicals made are relatively small compared to when they are dramatically scaled up for manufacturing. It has recently been suggested  that the pharmaceutical industry has perhaps adopted green chemistry as enthusiastically as it has because it has the most to gain because their manufacturing plants generate 25 to 100 times more waste than product.

We feel these global neglected and rare disease researchers would benefit greatly from being informed about green chemistry principles early on and that this has not been considered by any of the major organizations driving green chemistry initiatives. To date we are the only researchers that have used mobile apps to communicate green chemistry concepts. Our first free green chemistry app communicated information on solvent selection and is called Green Solvents (available on iOS).
The proposed solution and how the Principles of Green Chemistry have been applied/implemented [300-450 word limit]:

One of us, Alex Clark, has previously developed a mobile chemistry aware platform (the Mobile Molecular DataSheet) which implements powerful cheminformatics features. The core functionality is based on solving the problem of providing a high quality chemical structure editor for a palm-sized mobile device with highly constrained input functionality. The functionality has been packaged in library form, and used as the basis for a number of other apps with more task-specific functionality including the current one. We have created a user interface via the ODDT app, for iOS-based devices (iPhone, iPod and iPad) that is “magazine-like”.  The user initially selects from a list of topics, and from there can flip through recently posted content. The app is free for anyone to use, and provides content-consumption features as its primary purpose. As it evolves, the app will also be used to participate in active content-sharing and social networking activities. We are capturing content on a server and make use of Twitter as the primary source (as a proof of concept), which is regularly polled and assimilated into the data collection. The service provides an API for accessing ODDT topics and content. As the project evolves, the server will be gradually augmented to recognize particular data sources and information streams, and provide value added functionality. Currently it is able to recognize chemical data such as molecular structures, reactions and datasheets.

The project is open to participation from anyone and provides the ability for users to make annotations and assertions, thereby contributing to the collective value of the data to the engaged community. Much of the content is derived from public sources, but the platform is also amenable to commercial data input. The technology could also be readily used in-house by organizations as a research aggregator that could integrate internal and external science and discussion. This could be extended further by accessing other APIs providing news and data feeds of relevance to a particular area of interest. As the project evolves, social networking features will be developed for organizing participants into teams, with various forms of communication and content management possible.

A recent consortium organized by the American Chemical Society Green Chemistry InstituteTM (ACS GCI) Pharmaceutical Roundtable has developed a solvent selection guide publicly available on their website. The guide lists the 60 solvents by chemical name and rates the solvents against safety, health, air, water and waste categories with scores from 1 (few issues) to 10 (most concern). This information was previously used as the basis for the Green Solvents mobile app, developed after last years green chemistry and engineering conference. As an example this structure based table was tweeted with the #greenchemistry hashtag and is now saved in the ODDT database.

The state of testing of the underlying technology [300-450 word limit]:

We initiated an alpha version of the software in late February 2012, providing it to a dozen or so researchers with an interest in testing it. This provided an opportunity to address usability issues, fix bugs, and observe use patterns for scientists with a diverse range of experience with mobile and social networking software. Following the conclusion of the alpha test, we submitted the beta version to the iTunes AppStore, with the intention of growing the number of test users by making it freely available to anyone with an iOS-based device.

The mobile app was launched April 12th 2012. Initially we have used the app to harvest Twitter feeds on the hashtags described above for the diseases: malaria, tuberculosis, Chagas Disease, Leishmaniasis, Huntington’s disease, HIV/AIDS, and Sanfilippo syndrome as well as the research topic green chemistry. All of these subjects have high potential for positively impacting the research environment using computational approaches and dissemination information via mobile apps. We have used Twitter to feed content into these topics, by providing links to molecules and links to structure-activity tables. We have added the ability to endorse or reject tweets, expanded the number of topics by adding as well as a topic for information on ODDT. In addition the ability to visualize a thumbnail image for each tweet was added, as well as recognition of linked images. The app can now be used to manage multiple twitter accounts for the user. We also added the ability to summarize the endorsement and rejection activity for the user, arranging the topics on the screen from most to least used. The entry screen to the app displays the topics ranked by use. Tapping a topic image opens the topic browser, starting with the incoming page. Newly added content is listed on the right. Each tweet that has been introduced into the data collection is referred to a factoid. A factoid can be endorsed or disapproved, and the hyperlinks can be followed. The recent page shows factoids with one or more vote while the content section shows the most popular voted content in rank order. Molecule thumbnails can be tapped to open in other apps. Back on the entry screen, tapping the statistics summary button opens a listing of endorsements, disapprovals, injections and retirements for each hashtag.

The time to market [300-450 word limit]:

In late January 2012 the Pistoia Alliance (a pre-competitive initiative in which pharmaceutical companies and software vendors are attempting to develop standards that can be used by all companies) asked for participants in a Dragon’s Den ice breaker held at the Royal Society of Chemistry (http://www.collabchem.com/2012/02/07/dragons-den-pistoia-project-inspired-by-scio12/) . They wanted to gather ideas for a new external “R&D Service” that would transform the Pharmaceutical R&D sector and that would be in production and fit-for-use in 2015. Attendees included those from pharmaceutical companies, software companies, and venture capital funders. The ODDT app was developed in time to show a prototype (within 2 weeks). We shared our concepts and ideas in blogs including the incremental development and work in progress iterative reports associated with the technology development. We have described this work and the development of this app at several meetings including the American Chemical Society and will continue to promote its use in the scientific communities appropriate for each hashtag. From app idea to submission and approval at the iTunes AppStore took a little over 2 months. More information on the development of the app can be found at http://www.scimobileapps.com/index.php?title=Open_Drug_Discovery_Teams.

So that is some of what we had to submit..A first time for everything.

The next thing to do was update the scimobileapps pages for the app which was a bit overdue..sorry things have moved so fast I have not been able to keep up.

The final ODDT related work completed yesterday was a user guide and FAQ for the app. This was prompted after some great questions from one of our alpha testers (Jill Wood). After we completed this we posted it on Slideshare and FigShare. It was the first time I uploaded something on FigShare and I have to say it went well – really well and a day later it has had 168 views compared to less than 30 for Slideshare.

Well we are still learning and will see how we do with the business plan. So far its been a valuable learning process.

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