Need software developers to help with Algae Project!

[Jenney Choi - McNaughton]

Hi Biolab and Bioinformatics people, 

 

Since we have such a great pool of talented people in all our various community projects, I thought I'd ask, is there anyone who is interested in working on the Algae project?

We need software & systems people to help with the database, Arduino, and front-end web app stuff.

It's a really exciting project that involves developing technology that will use algae for bioremediation of polluted waters and creating biopolymers. 

For more information, please contact Sunny Allen (CC'ed on this e-mail).

You can also read more on our Google Group, https://groups.google.com/forum/?fromgroups=#!forum/plant-bio---algae-subgroup.

Thanks,

Jenney

[Barbara Collignon]

I can help for the mobile app.

[Barbara Collignon]

Can someone add me in biocurious-l...@googlegroups.com &
 biocurious-bi...@googlegroups.com ?

My answer got rejected from those groups.

Barbara

[Sunny Allen]

Hi everyone interested in helping us with the software side!  We really need you!

http://onlinebioreactor.org/?q=requirements

We want to build on what this guy has already accomplished, adding more arduino sensors, and further automating different sections of the bioreactor.  (We'll have sketches up of the bioreactor itself tomorrow.)

I'm a neophyte coder and I haven't done any Arduino stuff, so this is my weakest part of my understanding of the project.

Can some people offer advice about the best way to get our arduino data into a webserver/database, and then onto a website?

Currently the arduino data goes to a raspberry pi, and then ultimately to a MySQL database and a Heroku app, (those software people have stepped down from the project).  We're wondering if this can be done more simply and how.

Does any of that make sense?  I think it's time for me to sleep :)  I'll clarify further in the morning, and as we put together more details for the project.  Thank you again for everything!

Cheers,

Sunny

On Mon, Apr 15, 2013 at 8:14 PM, Jenney Choi - McNaughton <j3n...@gmail.com> wrote:

[Johan Sosa]

If it's already being placed into MySQL, making it into a simple website should not be difficult.  It can be likely be done with php or python.  I can check it out if you give me the info I need to look at the existing stuff. I am going to be at BioCurious everyday this week.

-Johan

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[Savitha Srinivasan]

The above link is broken but what you mentioned sounds very do-able. I would like to help out remotely.  Can you please share code(if any) along  with any specification docs. I am not familiar with arduino but I think we could find a way out. Can you also please add me on to your groups?

Thanks

Savitha 

f it's already being placed into MySQL, making it into a simple website should not be difficult.  It can be likely be done with php or python.  I can check it out if you give me the info I need to look at the existing stuff. I am going to be at BioCurious everyday this week.

-Johan

On Tue, Apr 16, 2013 at 1:45 AM, Sunny Allen <sunnic...@gmail.com> wrote:

[Barbara Collignon]

I believe that we need first to define what the mobile app will do  :

*Do you want an app that will crowdsource data from smartphones ?

*Do you want an app that will crowdcrunch data on smartphones ? 

*Do you want an app that will crowdsource & crowdcrunch data from/on smartphones ?

*Do you want an app that will only monitor the process from a website ?

According to the documentation from the onlinebiosensor website + the calibration/setup procedure via the I2C library (wire.h) 

as illustrated here: http://www.den-uijl.nl/electronics/gyro.html (very good link), I see several things :

You need to implement wire.h (i.e. the I2C libary) into Arduino Libraries. To do that, you need to connect Arduino to your PC and then install the library. The wire.h library will allow to detect the sensor & calibrate it, fetch the data and process the data.

You will need to calibrate the sensor yourself via APIs (e.g. setup()) and enter/write your own parameters/procedure. You will also need to develop additional APIs that will be sensor-specific (e.g. getPHReadings(myPhResult[])). 

One can then go forward with setting up the server side and assess how the whole system work (send data from sensor to server, add unit tests etc.). 

Later, as mentioned in the link I just provided, "It could be fun, when everything works, to port the software to the telephone and use that." 

Supposedly that you want to crowdsource data, how many times do you need to calibrate/recalibrate the sensor ? I may then need to reuse a piece of your code in the mobile app. A bluetooth connection should be enough to connect Arduino to a mobile phone. As well, I will need to implement in the client-server connection in the mobile app. So, we need to define the format of the data collected by the sensor/arduino (via smartphone) and the format of the data sent to the server (xml, jason ??). Also, we will need top define the client-server protocol which will depend on the server architecture & the security level you wish to achieve (Should we use REST or SOAP, encryption etc.) ? 

On the other hand, if it is a web app, then it makes sense to use PhoneGap. Then I will need the help of some javascript guys to build the js UI interface. What's cool with using PhoneGap is that you can deploy on all mobile platforms.  

Hope this helps,

Barbara

[Francisco McGee]

Barbara,

The stuff you mentioned on the I2C stuff re: arduino, I implemented such a workflow already that writes temp sensor data to txt file in csv; a perl script parses the csv into JSON and pushes that to a janky Postgres db on a NodeJS web app hosted here at heroku:

http://mysterious-crag-2552.herokuapp.com/

My friend Mike did the web app, I did the arduino stuff.

I can't support the dev because of school, but I can meet this weekend to turnover code an plot next steps. I know you guys are working out a brainstorming session soon.

Lemme know when you guys get a time for that, at BC office or Google hangout or whatever is cool too.

- Francisco

The poc is complete end-to-end, ie arduino --> web app, 

[Sunny Allen]

Thanks for your emails, Barbara and Francisco!

Barbara, wow, so many ideas.  We definitely want just a simple monitoring app to start out with but I'd love to eventually implement the more complicated ideas you have.

Francisco, we have to get our plan complete and the proposal out the door by Friday.  Can you send us the code you're already written so we know what's already been done?

I'm not sure that we want to stick with Heroku.  We want to integrate s much as possible with rhe webapp with mobile apps and with our WordPress blog.

PhoneGap sounds like a great way to go.

[Barbara Collignon]

Thanks Francisco for the update. You both did a great job !

Barbara

[Jonathan Reyles]

Folks,

What do you think about perhaps changing things up a bit and developing an Android app for the algae project? We can get members to build perhaps bits and pieces of code. This is also one possibility. This might also lead us to branch out with different ideas as well.

Again, just possibilities....

Jon

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Jon
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[Jenney Choi - McNaughton]

Maybe you can discuss it today in the meeting. I wanted you to keep it in mind. The Algae Team (BioMONSTAAAR) is planning to hold a Hackathon. The event details have to be fleshed out, but we would love for as many people as possible to be a part of it. 

[Sunny Allen]

We're not going to change anything in the actual proposal, so we can get it out on time tonight, but I think we should definitely discuss this.  After all, we already have Barbara on the team who'd like to build an iphone app!

Sunny

[Jonathan Reyles]