Team:BostonU/HumanPractices

From 2014.igem.org

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Latest revision as of 00:40, 18 October 2014

Policy and Practices

Working in the CIDAR lab space, our iGEM team quickly became interested in integrating technology with biology. Once we were introduced to the topic of bio-design automation (BDA), we became curious about the current state of the art for BDA. We wanted to know not only if there were workflows for integrating computational tools into wet lab work, but also how much these tools are actually used in the lab. As we began thinking about a project, our leading question became: Can we develop a more integrated BDA workflow that is better than the current state of the art?

Fortunately, we were able to volunteer at a the sixth International Workshop on Bio-Design Automation (IWBDA) at the beginning of summer. This was the perfect opportunity to learn about the current state of Bio-Design Automation and identify obstacles to BDA integration. Through conversation with one of the conference's keynote speakers, Professor Orit Shaer, we also became interested in answering the question: Can we integrate Google Glass into that workflow? (Refer to Google Glass section below).

IWBDA

As volunteers, we signed in the workshop speakers and attendants, helped with the posters, and set up the event venue. We were also able to attend the talks and poster presentations. This workshop was an important influencing factor on our project design. It gave us an opportunity to learn about the current research and concerns in the field, which shaped the direction and goals of our project.

One of the keynote speakers, Orit Shaer from Wellesley College, spoke about Human-Computer Interaction. She focused on tools that use reality-based interfaces and the considerations necessary for developing these tools. After listening to her presentation, we had the opportunity to talk with her. As a wetlab team interested in bio-design automation and experimental-computational integration, we thought it would be valuable to continue collaboration with Dr. Shaer’s lab at Wellesley. Her lab develops software tools for education and use in the wet lab.

One of the talks at the conference was given by Dr. Jacob Beal from BBN Technologies. He talked about the evolution of the TASBE Tools from when it was introduced to now, when the TASBE Tools is commonly used to predictively design constructs in mammalian cells. The past BU iGEM teams had used the Tools and our adviser, Dr. Haddock was very familiar with it, but that talk made us, the teammates, believe in potential of the TASBE Tools in the testing of constructs in E. Coli and the significance of predictive and accurate design. The talk was, thus, very influential in strengthening our motivation for the Chimera Workflow.

In addition to the talks and poster sessions, the IWBDA workshop included discussion sessions amongst all of the attendees. Topics focused on how to overcome the miscommunications between biologists and computer scientists as well as how to promote bio-design automation in our education systems. These discussions allowed us to talk more informally with the presenters and exchange our opinions and suggestions. We were also able to hear about current problems that exist between experimental and computational efforts, which gave us ideas about what needs to be improved.

NEGEM

From this conference, we learned the value of bringing together researchers from different labs to discuss, learn, and educate each other. Because of this, we decided to host the Third Annual NEGEM . Several other Northeast iGEM teams (MIT, Harvard, Tufts, WPI, Rutgers) and Wellesley came to Boston University twice over the summer to present their projects, discuss, and receive feedback. Each team had fifteen minutes to present their overall project idea, progress, timeline, and future goals to the other teams. After each presentation, there would be a Q&A session where other students could offer troubleshooting advice, ask for clarification, or offer critiques. During our lunch breaks, we held question led discussions about technological difficulties each team faced and how bio-design automation (BDA) could solve these obstacles. Our lunch was sponsored by BDAC. In October, we will have a final NEGEM meeting. Each team will give a formal presentation, representative of how they will present at the iGEM Giant Jamboree. This will be an opportunity to give final advice about the project and how to present it. We will also have time to show off our Wiki pages and make any last minute changes before the wiki freeze.

Google Glass

Throughout the summer we met up with students from the Wellesley HCI Lab to teach them about biological concepts and lab protocols and to learn about their projects. In past collaborations with Wellesley, our iGEM teams have mostly used their surface projects. This year, the Wellesley lab had a new technology project, the Google Glass. Our team felt that the Google Glass could have practical applications to the wetlab. We thought it would be an ideal tool for doing hands-free checklists for protocols, so we worked with the Wellesley HCI Lab this summer to incorporate our protocols into the Glass platform. They were able to upload our miniprep and transformation protocols on the Google Glass, which allowed us to see the protocol step by step without carrying around our notebooks.

Alan using the Google Glass in the Wellesley HCI Computer lab

While we tested the Glass miniprep protocol over the course of a few weeks, we discovered some pros and cons to using the Glass in the lab. The pros of using Glass: (1) it allowed us to go through a protocol without a printed paper copy, (2) it allowed us to take photos of our plates and tubes as we worked, and (3) it was lightweight and easy to wear. The cons of using Glass: (1) it heated up after 10-15 minutes of constant use, causing us to remove the Glass and thus preventing us from finishing a 45-minute protocol in one sitting, (2) we had to touch the side of the Glass with our gloved hands to progress through protocols, and (3) it didn't always respond to our motions when taking pictures. With these results in mind, we decided not to integrate Glass into the Chimera workflow. While Glass is not a part of our current workflow, we believe it could eventually become a very useful tool in the wetlab.

We were also able to provide a “client prospective” for the Wellesley HCI Lab's projects. Since they are developing software for use in the lab, we helped them decide which features would be most useful and improvements that could make their products more appealing.

Our Sponsors

@@ Line 13: / Line 13: @@
      <table width="100%" border="0" cellspacing="15" cellpadding="0">
   <tr>
-     <th rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/9/93/8158PPYAWiki.JPG"  width="300" style="float:right" style= "margin-left:10px"></th>
+     <td rowspan="2" scope="col"></td>
-     <th scope="col"> Working in the CIDAR lab space, our iGEM team quickly became interested in integrating technology with biology. Although we hadn't heard of bio-design automation, we wanted to learn how to use the computational tools developed in CIDAR to help us with our wetlab work. Fortunately, towards the beginning of summer, we were able to volunteer at a the  sixth International Workshop on Bio-Design
+     <td scope="col"> Working in the CIDAR lab space, our iGEM team quickly became interested in integrating technology with biology. Once we were introduced to the topic of bio-design automation (BDA), we became curious about the current state of the art for BDA. We wanted to know not only if there were workflows for integrating computational tools into wet lab work, but also how much these tools are actually used in the lab. As we began thinking about a project, our leading question became: <strong>Can we develop a more integrated BDA workflow that is better than the current state of the art?</strong> <br><br>Fortunately, we were able to volunteer at a the sixth International Workshop on Bio-Design Automation (<a href="http://www.iwbdaconf.org/2014/">IWBDA</a>) at the beginning of summer. This was the perfect opportunity to learn about the current state of Bio-Design Automation and identify obstacles to BDA integration. Through conversation with one of the conference's keynote speakers, Professor Orit Shaer, we also became interested in answering the question: <strong>Can we integrate Google Glass into that workflow?</strong> (Refer to Google Glass section below).
-Automation (<a href="http://www.iwbdaconf.org/2014/">IWBDA</a>).  <br><br> </th> </tr> </table>
+ </td> </tr> </table>
+<ul><ul>
+<tr>
+<td colspan="2" scope="col"><br><h3>IWBDA</h3></td>
+</tr>
      <table width="100%" border="0" cellspacing="15" cellpadding="0">
   <tr>
-     <th rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/9/93/8158PPYAWiki.JPG"  width="300" style="float:right" style= "margin-left:10px"></th>
+     <td rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/9/93/8158PPYAWiki.JPG"  width="300" style="float:right" style= "margin-left:10px"></td>
-     <th scope="col">As volunteers, we signed in the workshop speakers and
+     <td scope="col">As volunteers, we signed in the workshop speakers and attendants, helped with the posters, and set up the event venue. We were also able to attend the talks and poster presentations. This workshop was an important influencing factor on our project design. It gave us an opportunity to learn about the current research and concerns in the field, which shaped the direction and goals of our project.  <br><br></td>
-attendants, helped with the posters, and set up the event venue. We were also able
-to attend the talks and poster presentations. This workshop was an important
-influencing factor on our project design. It gave us an opportunity to learn about the
-current research and concerns in the field, which shaped the direction and goals of
-our project.  <br><br></th>
    </tr>
@@ Line 36: / Line 30: @@
 <table width="100%" border="0" cellspacing="15" cellpadding="0">
-<th rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/1/1e/XSC_8472YABUWIki.JPG"  width="300" style="float:right" style= "margin-left:10px"></th>
+<td rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/1/1e/XSC_8472YABUWIki.JPG"  width="300" style="float:right" style= "margin-left:10px"></td>
       <tr>
-         <th>
+         <td>
 One of the keynote speakers, Orit Shaer from Wellesley College, spoke about
@@ Line 45: / Line 39: @@
 and the considerations necessary for developing these tools. After listening to her
-talk, we had the opportunity to talk with her. As a wetlab team interested in bio-design
+presentation, we had the opportunity to talk with her. As a wetlab team interested in bio-design
   automation and experimental-computational integration, we thought it
@@ Line 53: / Line 47: @@
 lab develops software tools for education and use in the wet lab.
-</tr></th>
+</tr></td>
 </table>
 <table width="100%" border="0" cellspacing="15" cellpadding="0">
-<th rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/8/87/XSC_8600YABUWiki.JPG"  width="300" style="float:right" style= "margin-left:10px">
+<td rowspan="2" scope="col"><img src="https://static.igem.org/mediawiki/2014/d/dd/PP1YABUWiki.JPG"  width="300" style="float:right" style= "margin-left:10px"></td>
-<capt> Alan using The Glass in the Wellesley HCI Computer lab </capt></th>
+     <tr>
-<tr><th>
+        <td>
- Throughout the summer we met up with students from Wellesley to learn about their projects and
+One of the talks at the conference was given by Dr. Jacob Beal from BBN Technologies. He talked about the evolution of the TASBE Tools from when it was introduced to now, when the TASBE Tools is commonly used to predictively design constructs in mammalian cells. The past BU iGEM teams had used the Tools and our adviser, Dr. Haddock was very familiar with it, but that talk made us, the teammates, believe in potential of the TASBE Tools in the testing of constructs in <i>E. Coli</i> and the significance of predictive and accurate design.  The talk was, thus, very influential in strengthening our motivation for the Chimera Workflow.
-to teach them about biological concepts and lab protocols. We tested out the Google
+</tr></td>
+</table>
-Glass for several weeks and gave them feedback on the features they have been
-developing. For example, they were able to upload our protocols on the Google
-Glass, which allowed us to see the protocol step by step without carrying around
-our notebooks. We were also able to provide a “client prospective” for their projects.
-Since they are developing software for use in the lab, we helped them decide which
-features would be most useful and improvements that could make their products
-more appealing.
-</tr></th>
-</table>
 <table width="100%" border="0" cellspacing="15" cellpadding="0">
-<th rowspan="2" scope="col">
+<td rowspan="2" scope="col">
 <img src="https://static.igem.org/mediawiki/2014/6/60/8409YABUWIki.JPG"  width="300" style="float:right" style= "margin-right:10px">
-</th>
+</td>
-<tr><th>
+<tr>
+        <td>
 In addition to the talks and poster sessions, the IWBDA workshop included
@@ Line 101: / Line 85: @@
 about what needs to be improved.
-</tr></th>
+</tr></td>
 </table>
+<tr>
+<br>
+<td colspan="2" scope="col"><br><h3>NEGEM</h3></td>
+</tr>
 <table width="100%" border="0" cellspacing="15" cellpadding="0">
-<tr><th scope = 'col' colspan="2">
+<tr>
+<td rowspan="2" scope="col">
+<img src="https://static.igem.org/mediawiki/2014/0/04/NEGEM9BUWikiYA.jpg"  width="300" style="float:right" style= "margin-right:10px">
+</td>
+<td scope = 'col' colspan="2">
 From this conference, we learned the value of bringing together researchers
 from different labs to discuss, learn, and educate each other. Because of this, we
-decided to host the Third Annual NEGEM. Several other Northeast iGEM teams (MIT,
+decided to host the Third Annual <a href="https://2014.igem.org/Team:BostonU/NEGEM"> NEGEM </a>. Several other Northeast iGEM teams (MIT,
 Harvard, Tufts, WPI, Rutgers) and Wellesley came to Boston University twice over
@@ Line 137: / Line 132: @@
 wiki freeze.<br>
-</th>
+</td>
   </tr>
 </table>
+<tr>
+<br>
+<td colspan="2" scope="col"><br><h3>Google Glass</h3></td>
+</tr>
+<table width="100%" border="0" cellspacing="15" cellpadding="0">
+<tr><td scope="col">
+ Throughout the summer we met up with students from the Wellesley HCI Lab to teach them about biological concepts and lab protocols and to learn about their projects. In past collaborations with Wellesley, our iGEM teams have mostly used their surface projects. This year, the Wellesley lab had a new technology project, the Google Glass. Our team felt that the Google Glass could have practical applications to the wetlab. We thought it would be an ideal tool for doing hands-free checklists for protocols, so we worked with the Wellesley HCI Lab this summer to incorporate our protocols into the Glass platform. They were able to upload our <a href="https://static.igem.org/mediawiki/2014/b/b1/Epoch_Miniprep_BU14.xls">miniprep</a> and <a href="https://static.igem.org/mediawiki/2014/6/6a/Transformation_BU14.xls">transformation protocols</a> on the Google Glass, which allowed us to see the protocol step by step without carrying around our notebooks. </td>
+<td scope="col"><img src="https://static.igem.org/mediawiki/2014/8/87/XSC_8600YABUWiki.JPG"  width="300" style="float:right" style= "margin-left:10px">
+<capt> Alan using the Google Glass in the Wellesley HCI Computer lab </capt></td></tr>
+<tr><td scope="col" colspan="2">
+<br><br>While we tested the Glass miniprep protocol over the course of a few weeks, we discovered some pros and cons to using the Glass in the lab. The pros of using Glass: (1) it allowed us to go through a protocol without a printed paper copy, (2) it allowed us to take photos of our plates and tubes as we worked, and (3) it was lightweight and easy to wear. The cons of using Glass: (1) it heated up after 10-15 minutes of constant use, causing us to remove the Glass and thus preventing us from finishing a 45-minute protocol in one sitting, (2) we had to touch the side of the Glass with our gloved hands to progress through protocols, and (3) it didn't always respond to our motions when taking pictures. <b>With these results in mind, we decided not to integrate Glass into the Chimera workflow. While Glass is not a part of our current workflow, we believe it could eventually become a very useful tool in the wetlab.</b>
+<br><br>We were also able to provide a “client prospective” for the Wellesley HCI Lab's projects. Since they are developing software for use in the lab, we helped them decide which features would be most useful and improvements that could make their products more appealing.
+</tr></td>
+</table>
    </maincontent>
 </div>