Difference between revisions of "Team:Michigan Software/HP/Silver"

(Added the 2017 season's content)
Line 23: Line 23:
 
               <br>
 
               <br>
 
               <p>
 
               <p>
−
               <h1 class="grey-text heading-weight" align = "center">Protocol Model Development</h1>
+
             
 +
               <p id = "doubleSpace" class="p-font grey-text"> Our Human Practices efforts this year have been quite fruitful. We have made more outreach connections this year, and gained valuable insight into how scientists use our software. Our goal was to expand our user base, and through our beta testing efforts we have more users and protocol than ever before.
 +
              </p>
 +
              <br>
 +
              <br>
 +
              <br>
 +
              <br>
 
               <p>
 
               <p>
−
                  <br>
+
              <h1 class="grey-text heading-weight" align = "center">ProtoCat Beta Testing</h1>
 +
              </p>
 +
              <br>
 
               <div class="row" style="border-bottom:thin solid;"></div>
 
               <div class="row" style="border-bottom:thin solid;"></div>
 
               <br>
 
               <br>
 
               <br>
 
               <br>
−
               <p id = "doubleSpace" class="p-font grey-text">Prior to beginning the development of ProtoCat 3.0, we did research
+
               <p id = "doubleSpace" class="p-font grey-text">Several teams have given us quite valuable feedback on ProtoCat through our beta testing initiative. We reached out to fellow iGEM teams and requested their assistance with testing ProtoCat, as students of biology and other sciences would better be able to evaluate whether or not ProtoCat is truly a useful service than the computer science students who designed it. The teams evaluated the software on several fronts: our Search Function, the Upload Process, the Category System, the User Page, and the Protocol itself. After they provided us with feedback, we gave them assistance with their wikis.
−
                  on currently used protocol models. We began by brainstorming with members of our team who had
+
−
                  lab experience to get a foundation upon which we could improve. We tested the robustness of
+
−
                  this initial model by trying to represent the protocols uploaded to ProtoCat 2.0 with our new
+
−
                  model, tweaking and updating it along the way. Once we felt our model could adequately handle
+
−
                  the protocols we anticipated in ProtoCat 3.0, we met with our adviser, Dr. Santiago Schnell,
+
−
                  and ran our protocol model by him. Taking his feedback, we went back and further refined our
+
−
                  model to the one that we use in our current implementation of ProtoCat 3.0.
+
 
               </p>
 
               </p>
 
               <br>
 
               <br>
 +
              <br>
 +
              <br>
 +
              <p>
 +
              <h1 class="grey-text heading-weight" align = "center">Menlo Innovations Meeting</h1>
 +
              </p>
 +
              <br>
 +
              <div class="row" style="border-bottom:thin solid;"></div>
 +
              <br>
 +
              <br>
 +
              <p id = "doubleSpace" class="p-font grey-text">Additionally, we met with the founders of Menlo Innovations, a local Ann Arbor technology business to discuss the future of ProtoCat, namely, ways to make our product more sustainable and get it adopted by more users. They were able to offer us quite useful advice that we will keep in mind as we continue to grow and develop not only our software, but our team.
 +
              </p>
 +
              <br>
 +
              <br>
 +
              <br>
 +
              <p>
 +
              <h1 class="grey-text heading-weight" align = "center">iGEM North American Upper Midwest Meetup</h1>
 +
              </p>
 +
              <br>
 +
              <div class="row" style="border-bottom:thin solid;"></div>
 +
              <br>
 +
              <br>
 +
              <p id = "doubleSpace" class="p-font grey-text">This year we also attended the first iGEM North American Upper Midwest Meetup with Michigan Synthetic Biology, Michigan State University iGEM and the Carroll High School iGEM team. At this meetup, teams got to know each other while touring the scenic Michigan State University campus, and had the chance to practice presenting their projects to each other, receiving valuable feedback and having a great time!
 +
              </p>
 
               <br>
 
               <br>
 
               <br>
 
               <br>
 
               <br>
 
               <br>
 
               <p>
 
               <p>
−
               <h1 class="grey-text heading-weight" align = "center">Standard Protocol Format</h1>
+
               <h1 class="grey-text heading-weight" align = "center">IIT Madras Collaboration</h1>
 
               </p>
 
               </p>
 
               <br>
 
               <br>
Line 49: Line 73:
 
               <br>
 
               <br>
 
               <br>
 
               <br>
−
               <p id = "doubleSpace" class="p-font grey-text">Standardization in synthetic biology has gained a lot of traction,
+
               <p id = "doubleSpace" class="p-font grey-text">Lastly, we have established a relationship with the iGEM team from IIT Madras this year.. During their work on their host organism database ChassiDex, they directed their data donors to upload their protocols to ProtoCat, further populating our database with protocol and increasing the usage of our software. They include the links to our database on the pages of their database as well.
−
                  such as the BioBrick and Registry of Standardized Biological Parts. However, the procedures
+
−
                  used to generate them tend to be diverse in nature, with a bacterial transformation
+
−
                  protocol likely requiring different information than a ligation protocol. Online protocol
+
−
                  repositories must account for such differences when creating their data models, which will
+
−
                  usually require either a simplified model (such as solely text-based) or a more arduous
+
−
                  upload process. These different models become a problem when trying to share protocols between
+
−
                  the repositories, because the formats that the protocols are stored in are not compatible and
+
−
                  require an external conversion tool to get from one format to the other. In order to begin
+
−
                  working towards a standardized protocol format format, we reached out to OpenWetWare and
+
−
                  Protocols.io, two well known protocol repositories. We have began discussing how we will
+
−
                  reconcile our respective protocol models in order to get the best protocol model. The first
+
−
                  steps have been taken to build a cooperative relationship and create a standard protocol that
+
−
                  will help make protocols even easier to use, test, review, and design.
+
 
               </p>
 
               </p>
 
               <br>
 
               <br>

Revision as of 21:59, 31 October 2017

Human Practices - Silver







Our Human Practices efforts this year have been quite fruitful. We have made more outreach connections this year, and gained valuable insight into how scientists use our software. Our goal was to expand our user base, and through our beta testing efforts we have more users and protocol than ever before.





ProtoCat Beta Testing




Several teams have given us quite valuable feedback on ProtoCat through our beta testing initiative. We reached out to fellow iGEM teams and requested their assistance with testing ProtoCat, as students of biology and other sciences would better be able to evaluate whether or not ProtoCat is truly a useful service than the computer science students who designed it. The teams evaluated the software on several fronts: our Search Function, the Upload Process, the Category System, the User Page, and the Protocol itself. After they provided us with feedback, we gave them assistance with their wikis.




Menlo Innovations Meeting




Additionally, we met with the founders of Menlo Innovations, a local Ann Arbor technology business to discuss the future of ProtoCat, namely, ways to make our product more sustainable and get it adopted by more users. They were able to offer us quite useful advice that we will keep in mind as we continue to grow and develop not only our software, but our team.




iGEM North American Upper Midwest Meetup




This year we also attended the first iGEM North American Upper Midwest Meetup with Michigan Synthetic Biology, Michigan State University iGEM and the Carroll High School iGEM team. At this meetup, teams got to know each other while touring the scenic Michigan State University campus, and had the chance to practice presenting their projects to each other, receiving valuable feedback and having a great time!




IIT Madras Collaboration




Lastly, we have established a relationship with the iGEM team from IIT Madras this year.. During their work on their host organism database ChassiDex, they directed their data donors to upload their protocols to ProtoCat, further populating our database with protocol and increasing the usage of our software. They include the links to our database on the pages of their database as well.