The summer was full of exciting new experiences and a lot of hard work. You can browse through our sweat and tears here.
We worked hard but it all paid off. We had fun, we made new friends. We did something new, we learned something new. It was an amazing journey.
All members of our team, who work in the lab, have had a safety training as a part of their studies. The training covered the following topics:
In our iGEM work we have only worked with non-toxic E. coli (K12 derivatives) and all the protein coding sequences that we have used in our project are non-hazardous. We did not create new protein coding sequences but instead we used sequences that are already available as Biobricks.
We got to work in the Bioprocess Technology lab of Aalto University. We had our own table and we got to use all the instruments in the department. We also did some measurements in the labs of VTT Technical Research Centre of Finland.
Oskari, Martina and Minttu excited in the lab.
We also needed a proper office space where we could work during the summer since not everyone was going to do lab work all the time (and there wasn't that much space in the lab either).
We managed to find the "Learning Hub Living Room (CHEM)" (Vuori Hub) in the building of Department of Materials Science and Engineering. Since it was summer, there weren't many people around to use the space and we made it our home. It was a very comfortable place to work in!
Photo of Vuori Hub by Stewart Dowden
Photos of Vuori Hub.
Being the first team in Finland, we wanted to make sure that we documented everything we did as rigorously as possible.
We have our lab notebook in PDF files. From these you will be able to find everything that was done in the lab on a specific date.
We borrowed a convention from the software development framework, Scrum. So, every day all the team members answered these three questions:
Each of us wrote the answers down on our online team tool (Flowdock). According to the answers, we then assembled a detailed description of every single working day during our official work months (from May 20th to the end of August). So if you really really want to read exactly what we did, here's 30 pages of text for you to check out:
We gathered the highlights of our project to the timeline below so you can effortlessly skim through the story of Aalto-Helsinki Bioworks! Lab things are on the right side, office stuff (and everything else) on the left.
25.10.2014
Perfecting everything and admiring our wiki which is totally done at this point. All's well, we can just relax before the Jamboree.
8.10.-17.10.2014
Even though we had started developing the wiki early, the freeze deadline somehow snuck up on us. So little time, so many things to do. And finishing the wiki wasn't even the only thing we had to do before going to Boston!
14.10.2014
Unfortunately, due to time running out we had to freeze the lab work. We couldn't quite finish our wet lab project. Still, after almost 5 months of continuous work in the lab, we can be proud of what we've achieved and learned during this project!
9.10.2014
We didn’t have time to sequence our new Biobricks before sending them to iGEM HQ but we wanted to sequence them anyway, just in case. The sequences were confirmed to be ok! We were really happy about this since we did have some doubts about synthesizing parts with PCR on our own.
8.10.2014
Getting ready for the Giant Jamboree!
6.10.2014
Finally we got our own Biobricks ready to be sent to iGEM HQ. We put them in a box and wished them a safe journey.
10.9.2014
Out of nowhere we were invited to do an interview for the national radio YLE! We talked about our project and showed the interviewer around our lab.
1.9.-30.9.2014
We had a lot of problems with one specific ligation. Every time time we tried, only one of the inserts seemed to ligate with the backbone and the PCR and restriction digestion results on the gel looked bizarre.
For the longest time we pondered what could be wrong with our protocols or parts but then with the help of a professor we figured out that the problem might be that we had repetetive sequences in both inserts. Apparently E. coli doesn't like having two similar sequences in the same plasmid and it splices the other one out.
8.10.2014
At this point everyone already had courses going but luckily the lab is right upstairs form the lecture halls so we could still continue working almost full time in the lab. We just needed to time everything perfectly so we could go listen to the lectures while we had incubations or PCRs running.
5.9.2014
We held a presentation about our project at VTT. It was the first time we presented ourselves to a real scienctific audience and we got some really good feedback from the researchers.
4.9.2014
We participated in an event called Pitch Night and Oskari gave an inspiring speech about following dreams and introduced our project to the audience which mostly consisted of middle-aged people. Pitch Night was part of the Thinkfest arranged by University of Helsinki in celebration of the university's 375th anniversary.
2.9.2014
To kick off the academic year, Aalto University hosts a party every year during the first week of school. Despite the name, it's not really a party but more of an exhibition to show all the cool stuff the university has to offer. Of course, we were there to represent our team and to tell people about iGEM and our project.
28.8.2014
We had another round of testing with a part of our prototype and the LEDrig. The results seemed really promising!
26.8.2014
We planned to go to an escape the room thing, but when all the suitable times are booked, Minttu took us bowling instead.
22.8.2014
It’s like our bacteria got their own personalized disco!
21.8.2014
We got to try a super cool programmable microscope. We wanted to see if our cells produced any GFP but unfortunately it turned out that all our cells were already dead so there was no GFP to be detected.
21.8.2014, 22.8.2014
We went to visit the observatorium during the Night of the Arts event in Helsinki. There were also massive soap bubbles and a man with a whole band setup in a baby carriage.
The next day we went back to playing pinball and Crash Team Racing because it was so much fun last week.
19.8.2014
We built the first part of the prototype and started testing!
18.8.2014
After a long while, our genes finally arrived. Now we could take them and other parts we had assembled and put the whole genetically engineered machine together.
18.8.2014
We met the event manager and event organizer of Heureka and came up with a synthetic biology weekend workshop we could organize in Spring.
They were very excited about us and everything we had to show and tell. They said that this is a perfect match for them and all the simulations, games, pictures fit perfectly into the workshop.
We hope to inspire young people to study synthetic biology in the future and let the older people know it exists. This will also be a perfect opportunity for the next year's iGEM Team to get involved and organize something together.
14.8.2014
Lassi took us to play pinball. It was surprisingly fun. We played a ton of Crash Team Racing too.
14.8.2014
Pietu had been busy making the LEDrig inspired by Tabor Lab. This is what the early version looked like. The LEDrig would be the tool to control our light sensitive bacteria.
8.8.2014
We met with The Academy of Finland's Center of Excellence HYBER 2014-2019. They wanted us to talk in their conference and support us.
In the evening Oskari took us to play laser tag! He was way better at it than anyone else.
7.8.2014
Marko Ahtisaari and Madeleine Abromowitz from MIT Media Lab came to visit our office and lab. We discussed about a possible pop-up media lab in Helsinki and threw some ideas in the air. We were also invited to go visit the actual MIT Media Lab in Boston when we go there for the Giant Jamboree.
5.8.2014
We got our first sequencing results that were in confusing .ab1-files. Then it turned out that Geneious makes analysing them incredibly easy. Most of the sequences looked good, some not so much.
1.8.2014
Instead of staying in our HQ and eating in the cafeteria next to it, Laura took us to eat fancy sushi. It was delicious and fun.
31.7.2014
We built the sequences to synthetize from scratch. They included the lambda repressor OR sites that we designed. We found out that the synthetisizing costs the same for 0-1000 nucleotides, so we include a few surrounding BioBricks to save on lab time. (The OR sites are fairly small.)
28.7.2014
We had a number of ligations ready for assembling and it turned out there was a sequencing lab like 5 kilometers away.
We sealed 16 samples into tubes and sent them off. We were left eagerly awaiting to see if the work this far had succeeded.
22.7.2014
We meet Tania, an ex-iGEMer from the one 2012 Amsterdam team. It was a great meeting and we finally got some validation that we're doing some things right.
In the evening Martina took us geocaching! It is amazing what can be hidden in completely plain sight.
22.7.2014
The new primers designed by Lassi arrived and we tested them in amplifying the backbones with PCR. The primers bind to the RFP insert instead of the prefix and suffix which have a palindromic site and can cause troubles. In the end we didn't use PCR amplification of backbones since we opted for gel purifying instead. However, we did submit the primers to the registry and you can find them here BBa_K1443003 and BBa_K1443004.
15.7.2014
We presented our idea to hundreds of people and held a booth for 6 hours.
14.7.2014
In the evening Mikko took us to watch The Skin I Live In, Scott Pilgrim vs. The World and The Grand Budapest Hotel.
14.7.2014
We had the lambda repressor figured out and integrated into our system. We started planning for the parts to be synthesized.
13.7.2014
We were working hard in the lab during July and got many new ligations done. At this point the lab had started to feel like a home already.
10-11.7.2014
Summer of Startups took us to visit the Startup people of Tallinn. We decided this was a practice trip for Boston, so we planned to have as much fun as possible. It was a great success and an unforgettable experience.
8.7.2014
We found out that the lambda repressor system would be perfect for our three-way switch idea. We figured out how it worked and how to include it in our gene circuit.
4.7.2014
We decided that as a group we should do something fun every week that has nothing to do with iGEM. Every team member had their own week to plan an activity and pull the team to the mandatory weekly having-fun moment.
So, Otto surprised us with a fruit juicer and a ton of fresh fruit. We spent the early morning happily drinking smoothies while working intensely on our project.
3.7.2014
As Niklas had never been in a lab before and he was eager to see what we do there, we took him in for the day and showed him all the cool stuff. He even got to try some pipetting (with water only, although it didn't seem to lessen his enthusiasm)!
2.7.2014
Because chimera is a term both in gene techonology and mythology, Laura decided (and others immediately agreed) that drawing a chimera for each member would be a cool idea. Everyone could decide three animals and a chimera would be drawn based on those.
To read more about the chimeras, head to "chimeras" section on the Outreach page.
1.7.2014, 2.7.2014
We got the idea of explaining synthetic biology as turning bacteria into superheroes from a meeting with Miki Honkavaara. We started working on a new pitch based on that.
Pietu finished the pitch the next day and presented it at Summer of Startups. It seemed to go over very well. People finally understood what we were doing.
25.6.2014
Our BioBrick Seeker had been mentioned on the official help page for a while. We only noticed it now.
We also wrote a small advertisement text for the Community page and got the Seekers featured there.
24.6.2014
We even checked it with a gel.
23.6.2014
The Summer of Startups people came to visit our lab and see what we’re actually doing.
13.6.2014
We found out that the Registry provides BBa_J04450 parts in different backbones, which could be used as destination plasmids. The red fluorescent protein insert makes it easier to screen out the background.
12.6.2014
We kept getting weird results from PCR so we tried to solve the issue by doing a gradient PCR with different annealing temperatures. Seemed like 55 °C would be the answer to our problems.
11.6.2014
We made our first colony PCR to test if the ligations seemed right. Unfortunately they didn’t. We decided to make linearized plasmid backbones to increase the efficiency.
10.6.2014
BioBrick Seeker had received attention on Twitter. People really seemed to like the tool.
9.6.2014
We were trying to advertise ourselves and get some kind of financial help and support for this project. It felt really difficult and time consuming. We also took some new pictures, a new group photo, for example.
9.6.2014
The backbones did't seem to be working right and the negative control kept growing. Not good.
The reason seemed to be that we hadn’t gel purified the backbone and it kept religating with itself.
5.6.2014
We made a ligation calculator to help us estimate the amounts of different plasmids to be digested. The calculator calculates how many microliters of miniprepped plasmid is needed to be digested in order to pipet 4 ul of each digestion mix to the ligation mix. Insert-plasmid ratio as well as vector mass fields could be changed if needed. Taking these two variables into account, the appropriate molar amount and then the mass amount of inserts are calculated using the information of their lengths. This tiny little excel tool really saved time in the lab during the summer.
30.5.2014
This process would be repeated about 50 times during the summer, but this was the first. Video link: http://www.youtube.com/watch?v=TI_EuzNIaPg.
30.5.2014
It started from the mild inconvenience of searching for BioBricks in the lab. Now we could search through this year's distribution effortlessly. Because it was so useful for us, we decided to share it to others, too.
27.5.2014
Cooool. There it was!
26.5.2014
We got our hands on the Biobrick plates and took the first piece out. This is where it all started.
23.5.2014
This time it did actually look cool! The actual website might still be available on http://aaltohelsinki.com/index_en.html: check it out!
20.5.2014
...by making plates. Not that mind-blowing, but very important.
19.5.2014
We got one desk from the laboratory. There was still someone else's stuff on it, but it was ours and we were going to do amazing things there.
9.5.2014
We got the eagerly awaited box from iGEM and the competition started to feel real. In the box we found plates full of Biobricks and other cool stuff like these pins!
22.4.2014, 25.4.2014, 28.4.2014
We met a few times to go over what we would say to the Summer of Startups panel, so that they would accept us to the program. This culminated on the 28th, when we had the interview. Our team leader tried to attend through Skype, but the panel didn't like it. We managed to pull through anyway, and the panel was very excited about us at the end.
They accepted us in the program.
10.4.2014
We presented ourselves and our initial ideas to a panel of experts, mostly researchers from VTT and the Viikki biocampus. The occasion went very well and there was a lot of interesting discussion. We noticed that we really can do cool things as a group.
10.4.2014
We presented our initial ideas to our advisor, Markus, in preparation for the expert meeting. We discussed what direction to go and what kind of an idea to pick.
30.3.2014
We made an introduction video of us so we could apply to Summer of Startups. It turned out pretty good! Video link: http://www.youtube.com/watch?v=LJX21WthZQg.
23.3.2014
The first version of our website was built. We wanted it to look cool. It didn't.
18.3.2014, 25.3.2014
Some brainstorming. Wild ideas. Rating the ideas. Then an unbelievably cool post-it gradient of all the ideas.
14.3.2014
The first team meeting was held on a Friday afternoon. Some of us met each other for the first time ever, some had met before already. We talked about the project and got to know each other.
5.3.2014 - 12.3.2014
Oskari was in the first job interview in his life, as the interviewer. He hoeld 19 more interviews during the week. Nine people were chosen to be in the final team.
31.1.2014, 5.2.2014
It seemed like the universities were into the idea.
28.8.2013
First e-mails about the idea were sent.
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