Team:BU Wellesley Software/Notebook/MichelleNotebook

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Hi!  I'm Michelle, and I don't have a notebook yet.
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<h6>Michelle's Notebook</h6>
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 +
<h2>June 3</h2>
 +
<h4>Bootcamp</h4>
 +
<p>At bootcamp, we have learned tons of biology in a matter of days.  As someone who hasn't taken biology in six years, I've had a hard time getting back into the mindset of learning biology as a subject, but I also remember much more than I expected to from my high school days.  The central dogma was a huge part of my high school experience.  I'm still adjusting to the idea that we can break into the central dogma&mdash;that we can alter DNA and change the DNA that will be created when the cell replicates, making more of the cells that were created by us.  It's a step beyond what I've thought about before, and I still feel overwhelmed by what I don't understand.</p><br>
 +
 
 +
<h2>June 10</h2>
 +
<h4>Surface Training</h4>
 +
<p>This week, I've been learning the basics of the programming that I'll be doing this summer.  I've never worked on the Microsoft Surface before, so I'll need a lot of practice before I can do any programming on my own.  It helps that I'll likely be pair programming all summer; between two of us who have relatively little C# experience, we can probably figure out most of our problems (and I'm sure we'll have many).</p><br>
 +
 
 +
<h4>Lab Notebook Background Observations</h4>
 +
<p>As a part of user-centered design, we need to figure out what functions the wetlab team will want from an electronic lab notebook.  To do so, we have been observing the team working in the wetlab, as well as sitting in on their lab meetings.  We hope that doing so will help us figure out what the team needs, and will help us design an application that is as useful as possible.</p><br>
 +
 
 +
<h2>June 17</h2>
 +
<h4>Lab Notebook Designs</h4>
 +
<p>This week, I've worked with Kathy to design some initial prototypes for what the electronic lab notebook might look like.  So far, we have ideas for most of the main screens, but we haven't gone into too much detail.  We're hoping to present these designs to the wetlab team next week and get some feedback from them.</p> <br>
 +
 
 +
<h4>Interview with George Church</h4>
 +
<p>I went with Orit and Kathy to an interview with George Church, where we asked what sorts of computational tools he used in his lab and what sort of tools he saw being useful for the future.  While this might not be as relevant for the work we're doing now, it's essential in looking to the future of our work.  We're trying to envision what will come next for the tools we're creating now, and that helps us figure out what the role is of the tool we're making now.  If we're making a tool that won't change much over time, then we need to do more work now to ensure that it will continue to function in the future; if the tool we're making is a stepping stone to a much larger tool, then the algorithm and interaction issues are much more important than the actual implementation.</p>
 +
<br>
 +
<h2>June 24</h2>
 +
<h4>Lab Notebook Design Refinement</h4>
 +
<p>We presented our designs for the electronic lab notebook to the wetlab team this week, and they were very excited and eager to help us.  While they worked in the lab, they came out to visit me and Kathy while they had down time between experiments.  We explained our designs to them, then invited any feedback they had.  This worked very well for us, because we got plenty of feedback from them, and working with smaller groups let us confirm trends: when all of the groups told us that they wanted a clear way to communicate the procedures that they had completed with their labmates, but didn't want it to intrude on their own work, we knew that was something we would have to incorporate.  Some of the wetlab members (especially Alberto) even pulled out their own notebooks and started to draw what their ideal notebook would look like.  That's exactly what we need to see: now we can make software that will fill all of his needs.</p><br>
 +
 
 +
<h2>July 1</h2>
 +
<h4>Meeting with Avi</h4>
 +
This week, we went to talk to Avi Robinson-Mosher, a researcher at the Wyss Institute at Harvard.  We're working through the designs for the electronic lab notebook, and we aren't sure what our future plans for it are.  It's possible that we could design something that would only be useful to our iGEM teams, because that's the people who we see all the time, but we want to design something that will be useful to a wide variety of users.  To that end, we showed it to Avi, who comes from a computer science background but is now doing biology research.  He talked about the uses that he has for a notebook, and it was useful to see the differences: he sees a great use for the protocols that he needs on a daily basis, but doesn't need to add information to his notebook throughout his day, preferring to enter his data in the evening.  He also uses a wiki at the moment, so it's an interesting exercise for us to think about the benefits that our system can provide over the system that he uses now.
 +
 
 +
<h2>July 8</h2>
 +
<h4>Wellesley-BU Software Brainstorming Meeting</h4>
 +
This week, most of the BU software team and all of the advisors came to Wellesley to discuss the software work that each side had done over the summer and how we could bring those two things together.  We weren't sure if there were clear counterparts between our team, but we figured it out pretty well before we broke for the day.  We also got to play Ultimate Frisbee together, which was a blast and something that needs to be repeated.
 +
 
 +
<h2>July 15</h2>
 +
<h4>Meeting with MIT iGEM Team</h4>
 +
We met with the MIT iGEM team to show them our designs for the electronic lab notebook and to watch them working in their lab.  It was interesting seeing the differences in their lab setup: they had a large office area just outside of their lab where they spent most of their time while waiting for other reactions to complete, where our wetlab team spends almost all of their time in the lab, even while waiting for some reaction to complete.  The MIT team had some interesting suggestions, including integrating Google Calendar or some other online system for scheduling, and providing some chat functionality, since they had labs in two different buildings and communication between the two consisted of calls and texts.  These are ideas that we will try to incorporate into our designs before we begin to program the notebook.
 +
 
 +
<h2>July 22</h2>
 +
<h4>Presentation</h4>
 +
We presented over the last two weeks to the rest of the CS, math, and astro students who are doing science center research this summer.  It was interesting to take our work out of the context of synthetic biology and defend it as computer science research; there are lots of things that are very important to the synthetic biology community, but that are counterproductive to traditional computer science research.  It's interesting to think of that as a problem with our research model, and to consider alternatives for the future.
 +
 
 +
<h2>July 29</h2>
 +
<h4>Writing Workshop</h4>
 +
Kathy and I went to a science writing workshop this week that I think will help me organize my thoughts on what we've done this summer.  We had to write a page-long description of our work for non-scientists, and it helped me figure out what parts of our work this summer would be important to the public.  I'm glad that there are things that I think will be interesting to the rest of the world.
 +
 
 +
<h2>August 5</h2>
 +
<h4>End of Summer Wrap-up</h4>
 +
This week, I've done lots of work related to the funding I get from Wellesley.  On Thursday, we had a poster session where we presented all of the work we've done this summer, so we had to prepare posters to explain our iGEM work to a broad audience and practice explaining our work to a variety of people, from social science researchers who are afraid that E. coli will kill them in their sleep, to biology professors who already understand all of the background science and want to see how our work could fit in to their own research and teaching needs.  The poster session went very well, and it was great to hear feedback from the people who walked by.  We had a Surface with Gnome Surfer Pro in front of our iGEM posters, so we could actually show people what we were talking about.  Hopefully, the posters we made will be a good jumping-off point for the work we'll do for the iGEM jamboree.
 +
 
 +
<h2>September Work</h2>
 +
<h4>Wiki Creation</h4>
 +
We've done a lot of work towards creating content for the wiki: adding cohesive information about each of our projects in addition to the notebook and figuring out how all of the different parts will work together as a cohesive whole.  I'm looking forward to the creation of our presentation and seeing all of the other teams' projects at the regional jamboree... I hope to learn interesting things and come away inspired for next year!

Latest revision as of 03:48, 29 September 2011

BU-Wellesley iGEM Team: Welcome


Michelle's Notebook


Contents

June 3

Bootcamp

At bootcamp, we have learned tons of biology in a matter of days. As someone who hasn't taken biology in six years, I've had a hard time getting back into the mindset of learning biology as a subject, but I also remember much more than I expected to from my high school days. The central dogma was a huge part of my high school experience. I'm still adjusting to the idea that we can break into the central dogma—that we can alter DNA and change the DNA that will be created when the cell replicates, making more of the cells that were created by us. It's a step beyond what I've thought about before, and I still feel overwhelmed by what I don't understand.


June 10

Surface Training

This week, I've been learning the basics of the programming that I'll be doing this summer. I've never worked on the Microsoft Surface before, so I'll need a lot of practice before I can do any programming on my own. It helps that I'll likely be pair programming all summer; between two of us who have relatively little C# experience, we can probably figure out most of our problems (and I'm sure we'll have many).


Lab Notebook Background Observations

As a part of user-centered design, we need to figure out what functions the wetlab team will want from an electronic lab notebook. To do so, we have been observing the team working in the wetlab, as well as sitting in on their lab meetings. We hope that doing so will help us figure out what the team needs, and will help us design an application that is as useful as possible.


June 17

Lab Notebook Designs

This week, I've worked with Kathy to design some initial prototypes for what the electronic lab notebook might look like. So far, we have ideas for most of the main screens, but we haven't gone into too much detail. We're hoping to present these designs to the wetlab team next week and get some feedback from them.


Interview with George Church

I went with Orit and Kathy to an interview with George Church, where we asked what sorts of computational tools he used in his lab and what sort of tools he saw being useful for the future. While this might not be as relevant for the work we're doing now, it's essential in looking to the future of our work. We're trying to envision what will come next for the tools we're creating now, and that helps us figure out what the role is of the tool we're making now. If we're making a tool that won't change much over time, then we need to do more work now to ensure that it will continue to function in the future; if the tool we're making is a stepping stone to a much larger tool, then the algorithm and interaction issues are much more important than the actual implementation.


June 24

Lab Notebook Design Refinement

We presented our designs for the electronic lab notebook to the wetlab team this week, and they were very excited and eager to help us. While they worked in the lab, they came out to visit me and Kathy while they had down time between experiments. We explained our designs to them, then invited any feedback they had. This worked very well for us, because we got plenty of feedback from them, and working with smaller groups let us confirm trends: when all of the groups told us that they wanted a clear way to communicate the procedures that they had completed with their labmates, but didn't want it to intrude on their own work, we knew that was something we would have to incorporate. Some of the wetlab members (especially Alberto) even pulled out their own notebooks and started to draw what their ideal notebook would look like. That's exactly what we need to see: now we can make software that will fill all of his needs.


July 1

Meeting with Avi

This week, we went to talk to Avi Robinson-Mosher, a researcher at the Wyss Institute at Harvard. We're working through the designs for the electronic lab notebook, and we aren't sure what our future plans for it are. It's possible that we could design something that would only be useful to our iGEM teams, because that's the people who we see all the time, but we want to design something that will be useful to a wide variety of users. To that end, we showed it to Avi, who comes from a computer science background but is now doing biology research. He talked about the uses that he has for a notebook, and it was useful to see the differences: he sees a great use for the protocols that he needs on a daily basis, but doesn't need to add information to his notebook throughout his day, preferring to enter his data in the evening. He also uses a wiki at the moment, so it's an interesting exercise for us to think about the benefits that our system can provide over the system that he uses now.

July 8

Wellesley-BU Software Brainstorming Meeting

This week, most of the BU software team and all of the advisors came to Wellesley to discuss the software work that each side had done over the summer and how we could bring those two things together. We weren't sure if there were clear counterparts between our team, but we figured it out pretty well before we broke for the day. We also got to play Ultimate Frisbee together, which was a blast and something that needs to be repeated.

July 15

Meeting with MIT iGEM Team

We met with the MIT iGEM team to show them our designs for the electronic lab notebook and to watch them working in their lab. It was interesting seeing the differences in their lab setup: they had a large office area just outside of their lab where they spent most of their time while waiting for other reactions to complete, where our wetlab team spends almost all of their time in the lab, even while waiting for some reaction to complete. The MIT team had some interesting suggestions, including integrating Google Calendar or some other online system for scheduling, and providing some chat functionality, since they had labs in two different buildings and communication between the two consisted of calls and texts. These are ideas that we will try to incorporate into our designs before we begin to program the notebook.

July 22

Presentation

We presented over the last two weeks to the rest of the CS, math, and astro students who are doing science center research this summer. It was interesting to take our work out of the context of synthetic biology and defend it as computer science research; there are lots of things that are very important to the synthetic biology community, but that are counterproductive to traditional computer science research. It's interesting to think of that as a problem with our research model, and to consider alternatives for the future.

July 29

Writing Workshop

Kathy and I went to a science writing workshop this week that I think will help me organize my thoughts on what we've done this summer. We had to write a page-long description of our work for non-scientists, and it helped me figure out what parts of our work this summer would be important to the public. I'm glad that there are things that I think will be interesting to the rest of the world.

August 5

End of Summer Wrap-up

This week, I've done lots of work related to the funding I get from Wellesley. On Thursday, we had a poster session where we presented all of the work we've done this summer, so we had to prepare posters to explain our iGEM work to a broad audience and practice explaining our work to a variety of people, from social science researchers who are afraid that E. coli will kill them in their sleep, to biology professors who already understand all of the background science and want to see how our work could fit in to their own research and teaching needs. The poster session went very well, and it was great to hear feedback from the people who walked by. We had a Surface with Gnome Surfer Pro in front of our iGEM posters, so we could actually show people what we were talking about. Hopefully, the posters we made will be a good jumping-off point for the work we'll do for the iGEM jamboree.

September Work

Wiki Creation

We've done a lot of work towards creating content for the wiki: adding cohesive information about each of our projects in addition to the notebook and figuring out how all of the different parts will work together as a cohesive whole. I'm looking forward to the creation of our presentation and seeing all of the other teams' projects at the regional jamboree... I hope to learn interesting things and come away inspired for next year!

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