Team:Calgary/20 July 2009

July M T W T F S S     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

Carol
Chinmoyee
Emily
Fahd
Iman
Jamie
Jeremy
Katie
Kevin
Mandy
Patrick
Prima
Stefan
Vicki

May M T W T F S S         1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

June M T W T F S S 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

July M T W T F S S     1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

August M T W T F S S           1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

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October M T W T F S S       1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31

• Transformed plasmid, pCS26 into Top 10 cells with NEB Quick Ligase Buffer and Antartic Phosphatase Buffer to verify if the E.coli cells are able to uptake the larger plasmid. We wanted to check the transformation efficiency of a 10KB plasmid. This was plated on LB+Kan plates.
• To prepare for making competent cells, we grew overnight cultures in 5 mL of LB broth of Top 10 cells and XL Gold Ultracompotent cells (Stratagene)

This morning I helped Carol and Jeremy work with Johnathon, Carol's high school student. We made LB+ CM 35 broth as well as AK, AC, C and K plates. We also gave him a tour (led by Jeremy) of the Health Sciences Centre and our labs. In the afternoon I read through the Ethics Webinar report online and did a write-up on the Ethics Webinar for Jamie for the July newsletter. I also edited some write-ups for Mandi that are going up on the Wiki to show our collaboration with both the U of A and U of L teams. Sequencing came back today and it looks like the B0015 terminator was not successfully cloned in. Because of this, tomorrow I will have to re-digest J13002-LuxOD47E and B0015 to try construction again. I will follow this with transformation and plating.

Today, I concentrated my energies at marketing our iGEM project and looking at the ethical aspect of our project. Here is a summary what I did today:

1) Visa Interview, came to work at 12.00

2) Prepared extra documents that head to be faxed to the US counsulate

3) E-mailed Charles River Labs a rejection thank you letter. I also called him to clearify abt the small donations and educational tools.

4) E- mailed at Leica Canada a rejection thank you letter.

5) I called Dr Adolfo Cotter at Neuro image inc. to reschedule th appoint ment which never took place on friday due to emergency drill.

6) Left a voice mail at Applied Biosystems/Lifetech technologies.

7) Called Boheringer Ingleheim. She PROMISED that she would inform me abt her response to the sponsorship package by Friday.

8) Called Critical Outcome technologies. I have e-mailed him a sponsorship package and i will contact him next week for his response

9) E-mailed a sponsorship package to Amgen Canada. I will be in touch with them for their response.

Growth of overnight cultures are needed for tomorrow's plasmid isolation and verification. No other experiments were performed.

Did most of the debugging on DNA extraction today (almost done). We had an excellent meeting at ICT discussing how to implement better guides, etc. to facilitate learning on our island, which we will be starting to do shortly, as the basics of each of the three sections are finished (lab is almost there).

Third lab mission was written up: from DNA extraction of genomic DNA to PCR with biobricking of a gene from that DNA, to restriction digesting with other components to build a circuit.

Compiled and wrote for the Alberta Regional Team meet-ups page, (https://2009.igem.org/Team:Calgary/News/Alberta_Events) which will be submitted to the iGEM summer activities page for the entire iGEM community to see.

Worked on wiki homepage, made some more icons for it.

Editted most news pages, gallery page, and started working on sponsors page. Team page is mostly done.

Retrospective Notebook: This entry was not written on this day, but derived later from working notes I made that day.

I was still encountering problems with the collisions that I was using for my messaging system. Using collisions to trigger interactions between my molecule objects is unavoidable, that's just the only way for it to work: they hit each other! Finally, I settled on the system I'm still using now: since it's impossible to determine just what an object has collided with, objects that care about interacting with others now broadcast their name and position to all objects that might be interested on collision. If, for example, a Promoter receives a collision message from an RNA Polymerase, it's up to the promoter to determine whether the RNAP is allowed to bind, and then whether it is close enough to the promoter to connect.

Also began to encounter problems with objects having multiple copies of the 'stay put' script, each in different prims within the object. One could end up in the unintuitive situation of clicking a multi part object several times, but failing to change its state. Fixed this problem by having the multiple stay put scripts in a single object message each other to stay synchronized, so that when one click makes the object physical, all the other scripts know that the next click should make it nonphysical (despite not receiving the first click themselves).

For marketing today: I called Company 1 – left a voicemail -> follow up tomorrow – no one has her contact info or they lied and refused to give it to me

Company 2 – left a voicemail after sending him the pkg on firday follow up on July 22

Company 3 - Pkg was sent to the President so I informed his assistant that we’re not looking for something big and that we’ve received donations ranging from $200 - $6000 so any donation is helpful.

Company 4 - left a msg –follow up july 21

Company 5 – left a voicemail and she emailed me back stating that due to the economic downfall, they were unable to help us this year. I sent a thank you letter and asked for contacts.

Company 6  the manager of Fundraising & sponsorship still hasn’t contacted me. However, the receptionist said that if they can’t get a hold of him for me or if he’s out of town they’ll give it to the Regional Manager to handle it. Follow up with them July 22

Company 7  sent sponsorship pkg on thrusday but no one got back to me so I called today and the person who deals with this told me that she thought we wanted money for travel so I told her that “it’s solely for lab purposes- and we’re seeking sponsorship to fund our project”. Then she asked me to resend it to her directly, so I resent it. Follow up with her July 22

Company 8 Couldn’t get hold of the person in charge – so follow up tomorrow

The community relations Associate for Life Tech replied back to my mail and said that they are unable to help us or any other iGEM teams this due to a very small budge and layoffs….and they’ve been receiving emails from a whole bunch of iGEM companies for sponsorship.

I also wrote up the email for Jay Ingram and I’ll have it checked by Jamie, Jeremy and Fahd tomorrow before I send to you guys to double check.

I didn’t call the following b/c I called them on Friday/Thursday and they wanted some time to think about our proposal so this is what I’m going to do: Company 9 – Follow up on July 24 Company 10 – looking over pkg-follow up july 21. Company 11- looking over pkg- follow up july 22. Company 12 – Follow up 22- still looking over pkg

Today was spent preparing the synthetic kingdom for the meeting at ICT with an educator friend of Sonja's. Mandy and I also showed the high school student that's with us for the week around second life. At the meeting we got quite a bit of insight on how to further improve our island.

For my portion:

• Have "exhibits"
• Have a narrative (why do we care?)
• Exploration should be more guided
• more engineered cells
• Tell people about what they are seeing
• Integrate tutorial
• Squid buddy that shows you around

I actually wrote part of my introduction today and put together an outline for the rest of the paper! It isn’t good (and I’m planning to re-work most of it tomorrow because I don’t like it), but at least it’s there – which means that I can make it good later. I’ve been having trouble accessing my RefWorks account, which I think has to do with my no longer being a student. I have been keeping track of the relevant references on a separate word file and on my BibTex file (and have inserted the relevant labels where necessary), so I’ll address the compilation part later