Difference between revisions of "Team:Amazonas Brazil/Software"

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               <h4 class="p">What's the boost?</h4>
 
               <h4 class="p">What's the boost?</h4>
 
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               <div>
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               <p class="p">Scientific community have been achieved great results using CRISPR-Cas9 mediated
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              <div class="">
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              genome editing techniques. While these methods are moving forward, some methodological
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               <p class="p">Protocols are a set of well-documented steps to perform an experiment. It is through protocols that scientists can abstract and engineer their solutions. This standardization is the key to make it possible for scientists from the other side of the globe to reliably reproduce, in their labs, the results obtained by another scientist.</p>
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                aspects related to this technique could be further improved to bring up this science
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               <p class="p">The algorithms are to Computer Science as protocols are to Biotechnology. Following the principles that jumpstarted the exponential growth of software development techniques, promoting reuse of code, peer review, and incremental development, the open source community revolutionized the way that software was being made and those principles can easily be translated to Biotechnology.</p>
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                revolution even more.</p>
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               <p class="p">In prokaryotes, the genome editing based on CRISPR/Cas9 machinery requires quite
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    <p class="p">Advances in the opening of biological 'codes' has already promoted unpreceded developments in biological systems engineering, the most remarkable is the easily accessible NCBI database, which allows anyone to access detailed genomic and proteomic information of various species.
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                laborious days of work in the lab due to the multi-plasmid based edition. The system is not standardized and, in some methodologies, more than one plasmid is demanded,
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</p>
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                each one carrying a part of the CRISPR/Cas9 apparatus. Other critical problem consists
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    <p class="p">We envision a future where the abstraction for the creation of bioengineered living beings becomes more open, enabling anyone with the proper equipment and care, to reproduce reliably experiments and develop solutions.
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              in the addition of a linear DNA carrying homologous arms to provide a donor
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</p>
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                DNA to insert information into the genome during the HDR repair via. However,
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    <p class="p"><b>How will we do this?</b></p>
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              the linear donor DNA system has low edition efficiency due to the action of DNA restriction
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    <p class="p">To make our library available we created a Web Application decoupled from our WebServer, named iProGRAm, iGEM Protocol Git Repository from Amazonas_Brazil team, to deliver an environment to create, store and share lab protocols. </p>
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                systems present in wild-type and E. coli strains, which can degrade the linear DNAs
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    <p class="p">Moreover, any current web based application can migrate their data to AlexAPI format and use this database in a unified fashion. And with their own customization many applications can share a common space. </p>
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              before integration into genome. All this demands plenty of time and a lot of wet lab
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      <p class="p">This protocols platform will be able to search, cite and create protocols in a easy and fast way, creating an ecosystem to bring people together and generate positive interactions, promoting scientific growth.</p>
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                hours of work. To verify this information, we got in touch with other iGEM's teams who
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    <p class="p"><b>How will it impact iGEM?</b></p>
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                had work with CRISPR/Cas9 in the previous years, you can check this outreach part with
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      <p class="p">We believe that having such space would help everyone in the development of their project, reducing the amount of time taken in project design plan and increasing the success rate of teams. Helping everyone to achieve their results on time to deliver to the competition.</p>
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                more details here.</p>
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      <p class="p">We were inspired by the open software practices that brought github.com to life and over the year has made a tremendous impact on how open source software is being developed. We hope that iProGRAm can be ourProgram and really impact igemers from around the world.</p>
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</div>
 
             </div>
 
             </div>
 
            
 
            

Revision as of 19:56, 1 November 2017

Wiki_iGEM_Amazonas

SOFTWARE

A platform to expand the iGEM Experience

CRISPeasy

Our perspective is to provide a bacterial genome editing vector based on BioBrick parts assembly easy to engineer as A, B, C… CRISPR.

What's the boost?

Protocols are a set of well-documented steps to perform an experiment. It is through protocols that scientists can abstract and engineer their solutions. This standardization is the key to make it possible for scientists from the other side of the globe to reliably reproduce, in their labs, the results obtained by another scientist.

The algorithms are to Computer Science as protocols are to Biotechnology. Following the principles that jumpstarted the exponential growth of software development techniques, promoting reuse of code, peer review, and incremental development, the open source community revolutionized the way that software was being made and those principles can easily be translated to Biotechnology.

Advances in the opening of biological 'codes' has already promoted unpreceded developments in biological systems engineering, the most remarkable is the easily accessible NCBI database, which allows anyone to access detailed genomic and proteomic information of various species.

We envision a future where the abstraction for the creation of bioengineered living beings becomes more open, enabling anyone with the proper equipment and care, to reproduce reliably experiments and develop solutions.

How will we do this?

To make our library available we created a Web Application decoupled from our WebServer, named iProGRAm, iGEM Protocol Git Repository from Amazonas_Brazil team, to deliver an environment to create, store and share lab protocols.

Moreover, any current web based application can migrate their data to AlexAPI format and use this database in a unified fashion. And with their own customization many applications can share a common space.

This protocols platform will be able to search, cite and create protocols in a easy and fast way, creating an ecosystem to bring people together and generate positive interactions, promoting scientific growth.

How will it impact iGEM?

We believe that having such space would help everyone in the development of their project, reducing the amount of time taken in project design plan and increasing the success rate of teams. Helping everyone to achieve their results on time to deliver to the competition.

We were inspired by the open software practices that brought github.com to life and over the year has made a tremendous impact on how open source software is being developed. We hope that iProGRAm can be ourProgram and really impact igemers from around the world.