Team:Cornell/notebook
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- | |text=After several hours of discussion, we decided on our 20 new members! Congratulations, Tim Abbott, Hannah Ajmani, Eric Appel, Ryan Ashley, Nupur Bhatt, Arun Chakravorty, Rebecca Chew, Sharlene Dong, Sara Gregg, Alex Han, Eric Holmes | + | |text=After several hours of discussion, we decided on our 20 new members! Congratulations, Tim Abbott, Hannah Ajmani, Eric Appel, Ryan Ashley, Nupur Bhatt, Arun Chakravorty, Rebecca Chew, Sharlene Dong, Sara Gregg, Alex Han, Eric Holmes, Daniel Leach, Oat Luengvarinkul, Jeffrey Ly, Andrew Moorman, Ritvik Sarkar, Mac Sennett, Prashant Sharma, Olya Spassibojko, Yoshiko Toyoda, and Kyle Wheeler! |
|author=Rafael | |author=Rafael | ||
}} | }} |
Revision as of 03:26, 14 August 2013
Notebook
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January
January 5th
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Applications for new Cornell iGEM members were due today-- we've got 57!
-Rafael
January 16th
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After an eternity of reading and a gigantic spreadsheet of evaluations, we're finally ready to start interviewing applicants-- 36 of them!
-Rafael
January 25th
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I'm really excited about having these new members on the team. There were many awesome interviews, but now we have to sit down and make hard decisions on who to take, as most of last year's members are graduating, so there's a limit to how many new members we can train. This is going to be a tough weekend.
-Rafael
January 27th
show technical details
After several hours of discussion, we decided on our 20 new members! Congratulations, Tim Abbott, Hannah Ajmani, Eric Appel, Ryan Ashley, Nupur Bhatt, Arun Chakravorty, Rebecca Chew, Sharlene Dong, Sara Gregg, Alex Han, Eric Holmes, Daniel Leach, Oat Luengvarinkul, Jeffrey Ly, Andrew Moorman, Ritvik Sarkar, Mac Sennett, Prashant Sharma, Olya Spassibojko, Yoshiko Toyoda, and Kyle Wheeler!
-Rafael
February
February 1st
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We had our first full team meeting today with all the new members, introducing them to the iGEM competition, and did an icebreaker we call speed-taboodunit! For the next week, they have the assignment of analyzing a previous iGEM project (in groups), and explaining what the project was trying to accomplish, whether synthetic biology was a good approach for this, and reasons for their success or lack thereof.
-Rafael
February 7th
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Our first social event tonight went well! Hopefully with a few more of these we'll have some great team comradery and feel more comfortable around each other.
-Rafael
February 9th
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At our second team meeting we went over the past project analyses, as well as some biology review-- mostly molecular cloning. For the next week, we've assigned more past projects for them to outline in more detail.
-Rafael
February 16th
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Today we went over literature review, went over the past project outlines, and gave a two-week problem-oriented brainstorming and project outline assignment. Now that each member has looked at several past projects and analyzed them, we're moving into brainstorming for this year's project and practicing the development of project pitches.
-Rafael
February 21th
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We just started working on the wiki! Our first assignment: figuring out how wiki templates work. With templates the website would become much easier to edit, but for some reason HTML and wiki text don't seem to work very well together...
-Nupur
February 23th
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For the second week of this assignment, we compiled the brainstormed ideas and had members pick which ones they wanted to explore further. We also had a movie night planned, but it fell through :(
-Rafael
February 28th
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Finally got templates to work! The trick was ending HTML right before wiki text, and starting HTML again right afterwards. Not very elegant, but it works.
-Nupur
March
March 1st
show technical details
We want to revamp the notebook page with a filter system that lets you sort by subteam. We set up the basic layout of the page, but writing the javascript is going to be another story.
-Nupur
March 2nd
show technical details
Groups over the previous week investigated phage therapy, piezoelectric bacteria, "sticky paper", logic gates / bistable switches, phytases, mycelia, and pressure-adaptive materials. We're keeping the results from those, but doing a second round of brainstorming over the next few weeks-- the idea is to allow the exploration of any ideas that arose while researching the previous round of ideas.
-Rafael
March 5th
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We just finished the javascript for filtering. Rafael also made cool subteam icons for the filter buttons.
-Nupur
March 6th
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I made a template for notebook entries and added styling to each entry.
-Nupur
March 9th
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We compiled our second round of ideas, including topics like methanotrophs, a CRISPR knockout system, and suppressor tRNA inducible expression systems. We also took our first team picture, and probably the only one that will have all of last year's and this year's members together!
-Rafael
March 29rd
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Spring break knocked out a couple of meetings, but it looks like some research was accomplished nonetheless! The phytase project idea is looking pretty promising-- it incorporates a lot of different disciplines, with stuff for our mechanical and electrical engineers to do, as well as modeling.
-Rafael
April
April 6th
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We've narrowed it down to four project ideas: smokestack reactors (capturing pollutants with bioreactors), incorporation of phytases into anaerobic digesters, mycelial materials, and using bacteria to address issues with artificial implantable kidneys.
-Rafael
April 10th
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We had a call today with Ecovative Design, a company that uses mushrooms to make a biodegradable styrofoam analogue-- our mycelial materials project idea would involve working with them to improve their product. It seems like our interests are aligned and that we should be able to work with them. Exciting!
-Rafael
April 13th
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This meeting was dedicated to project pitches from each of the four ideas, followed by voting on which project we should pursue. Some of our graduate advisors also attended to provide a more seasoned perspective on the viability of each project. After some deliberation and spreadsheet magic, we decided on mycelial materials!
-Rafael
April 20th
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Today we worked on team structure for the summer; Swati will be the overall team leader, with me and Mark coordinating wetlab, Olya taking meeting minutes, Mac running drylab, and Hannah will be managing human practices. Later on in the summer, we will also develop task groups. For the next week, we've also split into groups to research various aspects of the mycelial materials project.
-Rafael
April 26th
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We've compiled initial research on carotenoid pigments, transformation protocols, DNA that may be useful for a basidiomycete toolkit, and a few other topics. Over the next week we'll meet with several professors on campus who work with fungi to see what resources and advice they can provide.
-Rafael
May
May 4th
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We met with Professor Gillian Turgeon, who does fungal transformation with Cochliobolus heterostrophus, an ascomycotic corn pathogen. We can get a few of the genes we've been looking for from her, yay! We also met with Professor Teresa Pawlowska, who directed us towards some other fungi and resources for fungi, as well as provided some background on fungal biology. As for the rest of the semester, we're letting everyone off the hook-- we don't want anyone to fail their exams because of iGEM!
-Rafael
Week 1
(06/17 - 06/23)
June 18th
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We started bootcamp today, doing our first transformations with kit plate biobricks.
-Rafael
June 19th
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The second day of bootcamp had more activity-- we PCR-amplified a variety of parts to biobrick them and get ready for making composite parts later.
-Rafael
June 20th
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I finally started moving pages to the 2013 wiki! It's looking very empty right now, but Rafael made a gif of our logo with his mycodraw program to use as a homepage placeholder. We also decided to add a technical details section to each of our notebook entries so that we can separate the jargon from daily summaries.
-Nupur
June 20th
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On our third day of bootcamp, we taught new members how to run gels, do minipreps, and run digests, continuing our preparation of biobrick parts from the previous two days.
-Rafael
June 21st
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The javascript for toggling technical details took a bit longer than expected, but we finished it up today.
-Nupur
June 21st
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Continuing with bootcamp, we column-purified the digests of PCR products and gel-purified the digested pSB1C3 backbone, dephosphorylated, and ligated, resulting in our first batch of biobricks or pre-biobrick parts.
-Rafael
June 22nd
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I added a flyout to notebook entries authors with a picture, short description, and link to their bio on the team page.
-Nupur
June 22nd
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Our penultimate day of bootcamp was a light one-- we only transformed cells with the constructs we'd made over the past four days.
-Rafael
June 23rd
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We concluded bootcamp with colony PCRs to test whether each of the constructs was present. Unfortunately, the gels had no bands, so we grew overnight cultures and will screen the minipreps instead.
-Rafael
Week 2
(06/24 - 06/30)
June 24th
show technical details
I started working on a hypertexting script that will automatically recognize words on a page and add a flyout with a description. We can use this to recognize names for the author flyouts I implemented yesterday, as well as other keywords such as plasmid names and protocols.
-Nupur
June 24th
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We miniprepped our three constructs. Then we went back to sleep.
-Rafael
June 25th
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I fixed a problem with the hypertext script not looping, but broke something else that causes everything to crash. I'm going to sleep. I'll figure it out tomorrow.
-Nupur
June 25th
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We did another PCR from the miniprepped plasmids to confirm the right sizes of inserts, then sent them in for sequencing.
-Rafael
June 26th
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The script is now working on all browsers except for Internet Explorer.
-Nupur
June 27th
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We started cloning crt genes downsteam of the T7 promoter. Because the T7 promoter is too small to extract as a fragment, we're placing crt genes downstream, then transferring the promoter+gene fragments back to pSB1C3. Today we digested crtY and the T7 promoter plasmid, but the digestion of crtY failed.
-Rafael
June 28th
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We redid the digestion of crtY and the T7 promoter plasmid from yesterday, apparently successfully this time. We also started liquid cultures of pBARGPE1, a plasmid we got from the Fungal Genetics Stock Center.
-Rafael
June 29th
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Crossing our fingers, we gel extracted and ligated the ostensibly successful digests of crtY and the T7 promoter plasmid, and then transformed. We also digested crtI and crtB, other carotenoid genes that we will also be putting under the T7 promoter, and miniprepped the pBARGPE1 that had been grown up last night.
-Rafael
June 30th
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Unfortunately, there were no colonies on the transformation plate for T7+crtY, so we redid the digestions for those. We also digested TtrpC and nptII for the eventual cloning of a PtrpC+nptII+TtrpC construct (we have to put the parts together in reverse because nptII contains a PstI site, which we will be trying to remove as well). Gel extractions of digested crtI and crtB were also empty (insignificant concentrations), so these digestions were also redone, and all were run on a gel, which looked mostly okay.
-Rafael
Week 3
(07/01 - 07/07)
July 1st
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We finished the hypertexting script and fixed some miscellaneous problems. I think we can call this a wrap. The notebook page is officially done!
-Nupur
July 5th
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Rafael added badges to the headers of all of our wikis, and implemented a badge flyout that links them all together.
-Nupur
Week 4
(07/08 - 07/14)
Week 5
(07/15 - 07/21)
Week 6
(07/22 - 07/28)
Week 7
(07/29 - 08/04)
Week 8
(08/05 - 08/11)
August 7th
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We helped Ciencias-UNAM get set to transfer their HTML website to the wiki. Hopefully we'll get up a tutorial for what to look out for on here soon!
-Nupur