# Iron Chef SynBio

I registered last minute for the Mammalian Synthetic Biology Workshop and it was awesome. It was really neat to see all the research everyone’s doing.

I got to chat with Ron and Mariola, from iGEM 2011. Definitely a blast from the past.

Ron said he still shows my animation occasionally. Haha, sweet.

Irving Weissman gave a really cool stem cell keynote.

Alex said Irv is like the godfather of stem cell research. Very impressive!

I unexpectedly ran into Pete! I haven’t seen him in like maybe 6 years!

It was great catching up!

Alex also gave a talk! I really enjoyed the talk, not only because I’d never heard Alex give a talk before, but also he had a clear and fun delivery style.

He thanked his wife, Amy, in the credits slide which I thought was super cute.

I think it’s super cool when couples are involved in each others’ fields. Amy probably provides some extraordinary research feedback just like how Harry gives me a lot of feedback for my conference talks.

Anyhoo, mSBW3 was great event. I saw some old friends, learned some neat stuffs, and in general had a good time.

One wish: I wish the the slides from talks are posted online somewhere. A great feature software conferences is that a lot of talks are recorded and the talks’ slides are posted online. This way, the conference can benefit a greater community.

You’re probably familiar with the DNA bases A, C, G, T and how A is the complement of T and C is the complement of G, and vice versa.

A neat mental exercise is to find the complement of the degenerate bases like R which represents both A and G.

Suppose the complement of R is a base that represents the complement of A and the complement of G. The complement of A is T and the complement of G is C, so the complement of R is Y (a degenerate base that represents T and G).

Here’s a whole list of them. Try it out.

It’s fun to think of complement as an function.

You see neat patterns like, every degenerate has exactly one complement, so complement is a bijective function. The fixed points of complement are at S (represents C and G), W (represents A and T), and N (represents all the bases A, C, G, and T). In fact, there will always fixed points at degenerate bases that represent a even number of bases. This is true even if we expand out the original A, C, G, T to fictional bases like Q and Z (I made Q and Z up).

Basically I needed to do some analysis on the upstream promoter region of about 1200 human genes.

I wasn’t gonna download them one-by-one, and I didn’t want to get a database dump of the whole genome.

Luckily, there’s UCSC’s hgTable! (I love you guys)

So it hit up.

Paste in your list of genes.

Note: No commas at the end of lines

You can even toggle between many options, like genomic DNA or protein sequence, or a certain number of bases upstream and downstream of the gene.

The output will be in one giant FASTA file so if you’re getting the sequences of a lot of genes, you better download the gzip, ’cause it’ll take forever to load it in your browser (it’s on the order of 100MB).

Another note: you might get more than one sequence per gene, depending on what tables, groups, and tracks you select.

Have fun!

The Saccharomyces Genome Database is a really nice tool to get yeast gene info. I used it for the first time this past week.

Eventually I figured out you could retrieve multiple genomic sequences using YeastMine.

The YeastMine template query feature accepts comma separated genes.

The resulting genomic DNA sequences can then be exported to CSVs.

Seasoned SGD users probably already knew about this feature, but it took me a while to figure out (I did not have any luck searching for this topic).

Hopefully this post will save someone some time!

I’m super excited for the Wyss Retreat tomorrow!

It’ll be awesome to check out all the non-synbio projects happenin’ at the Wyss in a giant show-and-tell.

The event is invitation-only, and I believe the invitation said we can’t talk about what we see at the event.

But the organizers have provided a Twitter hashtag to encourage discussion.

Huh.

There were two awesome things that happened at the recent Wyss Meet n’ Greet.

The first was I got to try some Romanesco broccoli!

I’d really wanted to eat these ever since I found out about from Josh them many years ago. He described looking at a Romanesco broccoli as looking at infinity. Now I got to taste some infinity! (It tastes like regular broccoli.)

The second awesome thing was I reconnected with Lynda.

So when I’m in lab, I would sometimes see a really familiar person walk by. We would sort of stare at each other, trying to figure out where we’d seen the other person. She came up and introduced herself as Lynda in the Meet n’ Greet. Turns out she was in some of my classes way back!

Neat!

I now know she’s in the Yin lab, so I’m definitely gonna try to stop by and say hi whenever I see her around.

Su got dry erase paper to turn lab benches into white boards! Brilliant!

Some biologists hover near a bunsen burner when preparing bacterial glycerol stocks, others don’t.

I fall in the latter. I’m not a believer of the flame.

I have yet to see good evidence that “flame will create an air current that will keep its surroundings sterile.” I’ve also noticed no difference in my stocks, back when I made ~94 a week.

Nowadays, since many of my lab friends are believers of the flame, I feel like I’m doing something taboo when making stocks.

I’d love to be converted.

On the flip side, always question your protocols!

A couple years ago, we’d heard Brian was in George Church’s book, Regenesis.

Today, while stopping by a bookstore, I decided to check it out.

There he is!

😀

Pretty sweet!