Difference between revisions of "Team:Open Science Global/Software"

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                 So many engineering fields use many design-build-test-learn (DBTL) cycles to find optimal results. Biofoundries are the infrastructure that allows synthetic biology and biotechnology to utilize the DBTL as the main workforce of change for solutions in organism engineering. Automation is the key element inside Biofoundries allowing them to high-throughput a wide range of designs, experiments, tests that later will generate integrative reports to define if the desired goal is achieved. However, what should be the final objective for this software in Biofoundries? Well, in our perspective the future depends directly on the creation of autonomous biofoundries, especially the frugal ones.
 
                 So many engineering fields use many design-build-test-learn (DBTL) cycles to find optimal results. Biofoundries are the infrastructure that allows synthetic biology and biotechnology to utilize the DBTL as the main workforce of change for solutions in organism engineering. Automation is the key element inside Biofoundries allowing them to high-throughput a wide range of designs, experiments, tests that later will generate integrative reports to define if the desired goal is achieved. However, what should be the final objective for this software in Biofoundries? Well, in our perspective the future depends directly on the creation of autonomous biofoundries, especially the frugal ones.
 
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                <p>Autonomy is a concept that people are familiar with when talking about cars. Fully autonomous vehicles are the pinnacle of automation by transforming a very human-dependent activity into a completely automatic one. What if synthetic biology could be similarly automized? What if protocols could be executed by an integrated infrastructure? What if they could be adapted to each specific laboratory setup? What if the design of genetic parts and experiments could be corrected while being produced?</p>
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              <p>We understand that Frugal Biofoundries will need open software that allows for these types of integrations. Where the community actively communicates and develops their own non-proprietary, free, easy, high-quality software solutions, that could resolve a high-throughput and high volume of data. Not only that, we need synthetic biology developers that will develop the next generation of tools for biotech infrastructure.
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                 <p>n order to do that, we decided to utilize Poly, an open-source Go package for organism engineering. As a Go package, Poly has intrinsic properties that allow easy reusability, compatibility, and good performance. Poly also has a very vivid and funny community, guided by a very active maintainer and creator of the package, Timothy Stiles. The compromise of creating good quality code allied to the ambition to become the most complete and open collection of computational synthetic biology tools is what makes Poly a very attractive option for what we’re trying to create. Actually, most of the Friendzymes software team is or became a Poly contributor.</p>
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                Do you see any Teletubbies in here? Do you see a slender plastic tag clipped to my shirt with my name printed on it? Do you see a little Asian child with a blank expression on his face sitting outside on a mechanical helicopter that shakes when you put quarters in it? No? Well, that's what you see at a toy store. And you must think you're in a toy store, because you're here shopping for an infant named Jeb.
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                 <p>We decide for this MVP (Minimum Viable Product) part of Friendzymes projects to stipulate two main objectives:</p>
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                Your bones don't break, mine do. That's clear. Your cells react to bacteria and viruses differently than mine. You don't get sick, I do. That's also clear. But for some reason, you and I react the exact same way to water. We swallow it too fast, we choke. We get some in our lungs, we drown. However unreal it may seem, we are connected, you and I. We're on the same curve, just on opposite ends.
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             <h2 id="contribution">Contribution</h2>
 
             <h2 id="contribution">Contribution</h2>

Revision as of 20:49, 20 October 2021

Software
Title
Subtopic
INDEX
Subsite Subsite Subsite Subsite
Project
Introduction Model Contribution Proof of Concept Proposed Implementation Collaborations

Introduction

So many engineering fields use many design-build-test-learn (DBTL) cycles to find optimal results. Biofoundries are the infrastructure that allows synthetic biology and biotechnology to utilize the DBTL as the main workforce of change for solutions in organism engineering. Automation is the key element inside Biofoundries allowing them to high-throughput a wide range of designs, experiments, tests that later will generate integrative reports to define if the desired goal is achieved. However, what should be the final objective for this software in Biofoundries? Well, in our perspective the future depends directly on the creation of autonomous biofoundries, especially the frugal ones.

Autonomy is a concept that people are familiar with when talking about cars. Fully autonomous vehicles are the pinnacle of automation by transforming a very human-dependent activity into a completely automatic one. What if synthetic biology could be similarly automized? What if protocols could be executed by an integrated infrastructure? What if they could be adapted to each specific laboratory setup? What if the design of genetic parts and experiments could be corrected while being produced?

We understand that Frugal Biofoundries will need open software that allows for these types of integrations. Where the community actively communicates and develops their own non-proprietary, free, easy, high-quality software solutions, that could resolve a high-throughput and high volume of data. Not only that, we need synthetic biology developers that will develop the next generation of tools for biotech infrastructure.

A quick walk through on toolkit

n order to do that, we decided to utilize Poly, an open-source Go package for organism engineering. As a Go package, Poly has intrinsic properties that allow easy reusability, compatibility, and good performance. Poly also has a very vivid and funny community, guided by a very active maintainer and creator of the package, Timothy Stiles. The compromise of creating good quality code allied to the ambition to become the most complete and open collection of computational synthetic biology tools is what makes Poly a very attractive option for what we’re trying to create. Actually, most of the Friendzymes software team is or became a Poly contributor.

We decide for this MVP (Minimum Viable Product) part of Friendzymes projects to stipulate two main objectives:

Contribution

Your bones don't break, mine do. That's clear. Your cells react to bacteria and viruses differently than mine. You don't get sick, I do. That's also clear. But for some reason, you and I react the exact same way to water. We swallow it too fast, we choke. We get some in our lungs, we drown. However unreal it may seem, we are connected, you and I. We're on the same curve, just on opposite ends. Now that there is the Tec-9, a crappy spray gun from South Miami. This gun is advertised as the most popular gun in American crime. Do you believe that shit? It actually says that in the little book that comes with it: the most popular gun in American crime. Like they're actually proud of that shit.

Proof of Concept

Your bones don't break, mine do. That's clear. Your cells react to bacteria and viruses differently than mine. You don't get sick, I do. That's also clear. But for some reason, you and I react the exact same way to water. We swallow it too fast, we choke. We get some in our lungs, we drown. However unreal it may seem, we are connected, you and I. We're on the same curve, just on opposite ends.

Now that there is the Tec-9, a crappy spray gun from South Miami. This gun is advertised as the most popular gun in American crime. Do you believe that shit? It actually says that in the little book that comes with it: the most popular gun in American crime. Like they're actually proud of that shit.