[Openchemistry-developers] Interested in OneMol: Google Docs & YouTube for Molecules

[Geoffrey Hutchison]

Dear Siddhant,

Yes, state synchronization, live editing, comments, etc would be some of the key features for OneMol. I haven't gone through the Google real-time API, but that's certainly a core concept that would be needed.

Keep in mind that not everyone would want to upload public data, so security / visibility are important components too (e.g., in Google Docs, I can share the URL or invite others by e-mail, etc.).

We're looking forward to seeing a proposal.

Thanks and best regards,
-Geoff

---
Prof. Geoffrey Hutchison
Department of Chemistry
University of Pittsburgh
tel: (412) 648-0492
email: geoffh at pitt.edu
web: http://hutchison.chem.pitt.edu/

> On Mar 16, 2017, at 11:34 PM, Siddhant Karhadkar <s41997 at outlook.com> wrote:
> 
> Dear Sir,
>               I had a look at some of the existing repositories as mentioned by you like the PubChem, ChemSpider and PQR. All of them were for storage and viewing of molecular data. Some of them had the options for molecular data upload and view. So, I feel that OneMol in itself can have many dimensions and would be really helpful for the chem community. Some more features that can be added to the repositories other than upload and view are tagging, file-sharing and group/community project (Similar to ResearchGate). Google has released its Real-time API, it is useful for any kind of state synchronization and live editing, so can we use it for viewer state synchronization? I saw few apps which utilized Real-time API to build a Real-time code editor, Real-time cube player, etc. It may also be used to build google docs like live editor for editing chemical docs or papers. As most of the real-time API's are based on the principal of Operational Transformation.
> 
> Regards,
> Siddhant Karhadkar,
> Sophomore, 
> Department of Chemistry,
> Indian Institute of Technology, Kharagpur,
> West Bengal, India - 721302.
> Contact - 9932304649
> 
> 
> 
> 
> From: Geoffrey Hutchison <geoff.hutchison at gmail.com <mailto:geoff.hutchison at gmail.com>> on behalf of Geoffrey Hutchison <geoffh at pitt.edu <mailto:geoffh at pitt.edu>>
> Sent: 14 March 2017 20:28
> To: Siddhant Karhadkar
> Cc: dkoes at pitt.edu <mailto:dkoes at pitt.edu>; openchemistry-developers at openchemistry.org <mailto:openchemistry-developers at openchemistry.org>
> Subject: Re: Interested in OneMol: Google Docs & YouTube for Molecules
>  
> Dear Siddhant,
> 
> I think the specs are fairly clear:
> http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_OneMol:_Google_Docs_.26_YouTube_for_Molecules <http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_OneMol:_Google_Docs_.26_YouTube_for_Molecules>
> GSoC Ideas 2017 - wiki.openchemistry.org <http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_OneMol:_Google_Docs_.26_YouTube_for_Molecules>
> wiki.openchemistry.org <http://wiki.openchemistry.org/>
> Guidelines. Open Chemistry is an umbrella for projects in chemistry, materials science, biochemistry, and related areas. We intend to concentrate mainly on projects ...
> 
> 
> There needs to be:
> * A web repository for uploading files (e.g., similar to http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_Computational_Chemistry_Web_Repository <http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_Computational_Chemistry_Web_Repository>) including a REST API for upload and query.
> GSoC Ideas 2017 - wiki.openchemistry.org <http://wiki.openchemistry.org/GSoC_Ideas_2017#Project:_Computational_Chemistry_Web_Repository>
> wiki.openchemistry.org <http://wiki.openchemistry.org/>
> Guidelines. Open Chemistry is an umbrella for projects in chemistry, materials science, biochemistry, and related areas. We intend to concentrate mainly on projects ...
> 
> * A web front-end to view files using 3DMol.js
> * Some element of chat or collaboration thread for each file
> * An API to synchronize viewer state (in 3DMol.js) between the clients
> 
> That would be the beginning. Think further about what it might mean to have a "Google Docs" for chemistry and take a look at some existing chemistry repositories:
> * https://pqr.pitt.edu/ <https://pqr.pitt.edu/>
> PQR | Home <https://pqr.pitt.edu/>
> pqr.pitt.edu <http://pqr.pitt.edu/>
> Rather than viewing a static 2D picture, you can now choose an interactive 3D depiction from a database of thousands of molecules. Most importantly, PQR makes it easy ...
> 
> * https://openchemistry.kitware.com <https://openchemistry.kitware.com/>
> * http://www.chemspider.com <http://www.chemspider.com/>
>  <http://www.chemspider.com/>	
> ChemSpider | Search and share chemistry <http://www.chemspider.com/>
> www.chemspider.com <http://www.chemspider.com/>
> ChemSpider is a free chemical structure database providing fast access to over 34 million structures, properties and associated information.
> 
> * https://pubchem.ncbi.nlm.nih.gov/compound/2244 <https://pubchem.ncbi.nlm.nih.gov/compound/2244>
>  <https://pubchem.ncbi.nlm.nih.gov/compound/2244>	
> aspirin | C9H8O4 - PubChem <https://pubchem.ncbi.nlm.nih.gov/compound/2244>
> pubchem.ncbi.nlm.nih.gov <http://pubchem.ncbi.nlm.nih.gov/>
> aspirin | C9H8O4 | CID 2244 - structure, chemical names, physical and chemical properties, classification, patents, literature, biological activities, safety/hazards/toxicity information, supplier lists, and more.
> 
> * http://www.chemspider.com/Chemical-Structure.2157.html?rid=fa75a88c-65f2-43be-9a72-95bff61933f0 <http://www.chemspider.com/Chemical-Structure.2157.html?rid=fa75a88c-65f2-43be-9a72-95bff61933f0>
> 
> Best regards,
> -Geoff
> 
> ---
> Prof. Geoffrey Hutchison
> Department of Chemistry
> University of Pittsburgh
> tel: (412) 648-0492
> email: geoffh at pitt.edu <mailto:geoffh at pitt.edu>
> web: http://hutchison.chem.pitt.edu/ <http://hutchison.chem.pitt.edu/>
>> On Mar 14, 2017, at 4:16 AM, Siddhant Karhadkar <s41997 at outlook.com <mailto:s41997 at outlook.com>> wrote:
>> 
>> Hi,
>>     I am Siddhant, Sophomore, IIT Kharagpur, India. I am interested in the project of Development of prototype web service for web and desktop collaboration as well as the database connection. My interest in this project is because I have earlier developed a web service called IAFC, which was an AI based corruption database, which won the Accenture Innovation Jockeys Competition. The service was based on a Node.js server and used MongoDB as a database. We used Machine Learning to analyze any query entered by the user and then populated the database and rendered searches from the same. So, I am well acquainted with Javascript frameworks, express server, RESTful, MongoDB and have some basic knowledge of front-end services/frameworks(HTML, CSS, Jquery, AngularJS). Also, the service was hosted on IBM Bluemix, so I have a good understanding of such web platforms(Others being - Azure, AWS). I am always excited about building web services that can impact people and be useful as well as easier to handle. Kindly, guide me through the project deliverables so that I can express my views and get to know what can be expected from me. Looking forward to your guidance, 
>> ThankYou.
>> 
>> Regards,
>> Siddhant Karhadkar,
>> Sophomore, 
>> Department of Chemistry,
>> Indian Institute of Technology, Kharagpur,
>> West Bengal, India - 721302.
>> Contact - 9932304649

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