Ed's Big Plans

Computing for Science and Awesome

Meeting with Chris

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Brief: Met with Chris last week. Chris finished with the convergence tests and some cross validation sets on his descriptors and recommended his own design for 80/20 prediction tests… Meanwhile, I’ve updated the InChI grammar used for the NGN to work with the new data, and have set up experiments to run convergence tests using the SMILES-NGN and InChI-NGN on the eight possible QSAR datasets on SharcNet (16 processes total)… Next on the list– create a script to evaluate his preliminary cross validation experiments (based on Neural Network predicted vs. target values) and provide instructions for running the convergence tests with my NGN software… Will need to pull up an old nugget.py to wrap the convergence test (current one doesn’t halt and always runs 100 trials).

Soon: Port everything to Ubuntu Linux so that we can maintain compatibility without further porting care of Sun Virtualbox VM… Meeting again tomorrow…

oGEM: An iGEM Story

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Thursday last week, the Waterloo iGem team had a online conference over Skype with the iGem teams of Toronto and Ottawa. Also present was Andrew Hessel– the seeder of Canadian iGEM teams… It was pretty extensive, so I’ll just discuss the parts that ended up being immediate goals for the Waterloo team.

oGEM Meeting Over Skype

oGEM Meeting Over Skype

The objective is to end up making an Ontario federation in synthetic biology under the iGEM scaffold a reality; we would eventually expand out of iGEM and cover synthetic biology across Canada, but — plan small, think big.

There must also be incentives for being part of such a federation– an obvious answer is a network of distributed services which are greater as oGEM than the sum of its parts.

Plan Small, Think Big

One of the first things we can experiment on is the idea of a social engineering application. This feature is being investigated by the Waterloo team– Arianne has created a mock-up using Elgg. The objective is to allow individuals across oGEM to know what expertise exists in the network, and to contact appropriate users for collaboration or help based on the interests or skills listed by each user.

Sigma is for Summation

Incentive services for oGEM are being tackled by our team. Andre wants to introduce a federated database of strains and cultures (codenamed BioMortar)– whereas iGEM offers clonable biobricks, the issue remains that cellular transformation is not deterministic. It may work some of the time, or most of the time– for some teams, certain bricks just aren’t successfully cloned. This federation would allow the cataloging of living frozen strains in freezers across oGEM and if users are willing, all synthetic open-source strains. Eventually, someone seeking a strain they’ve had issues with would message someone with a working copy as it were, and request it be shipped.


We expect caveats to emerge– first of which is dedication. In our meeting, it is clear that working groups must emerge to take over tasks– working groups that are passionate about their own objectives. I suppose UWiGEM represents two working groups each operating on one of the above steps. Ottawa has volunteered to look at the legal caveats– how oGEM identifies itself as a legal entity as well as its level of permitted activity while still being a part of iGEM and synthetic biology across the nation is all very vague. It’s good that someone has an idea of how to investigate this feature of the problem terrain!

Group Photo

Attending the meeting on the Waterloo side…

oGEM Chat - Waterloo Side

oGEM Chat - Waterloo Side

Left to right in the above photo: Danielle, Andre, John, Leah.

iGEM: Freedom Unhashed

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An iGEM modeling meeting was held yesterday wherein Andre revealed his big plans for switching the team into enduserhood. Unfortunately, I didn’t follow along as well as I could have this time around and can really only document and comment on the bottom line.

We’ve again self-organized into two to three teams based on task. The first team is charged with creating a hashing function which creates a sequence of integrase usable tokens from an integer. The second (and third?) team is responsible for creating a check to ensure that a given product corresponds correctly to a given pair of reactant sequences. Finally, the dangling task of creating an even bigger external harness along with modifications to the present main.py program logic is likely being handled by the latter team.

The Hashing Task is kind of interesting because it essentially calls for unhashing an integer into a meaningful sequence rather than hashing a meaningful sequence into a unique integer. Since the reactant strings can themselves be lexicographically sequenced, then the task quickly becomes an enumeration or counting problem whereupon we find the most efficient way to count through the possible permutations of reactant tokens until we reach the integer that we want. The backward task (what we’re doing) may end up being implemented as the forward task with a sequential search.

The hashing subteam is headed by Jordan, the modeling head from last year and is joined by myself and Wylee– I honestly don’t see this as a task that can’t be completed by one person in a single bout of insanity– so it’s likely that I’ll hop over to Andre’s reactant-product verification team whenever this finishes.

We’ve planned another meeting for Tuesday 5pm next week to pull whatever we have together and to tackle any nascent problems.

Reactant-Product Verification is I think the more straight forward item, at least to explain. It is likely more technically challenging. Basically, we make the reaction go forward, and if the product matches what we wanted, then we favour the persistence of the product. … Err, at least that’s how I understood it… I’ll probably need to pop in and ask about it on Thursday before the big oGEM Skype meeting.

Side note– Oddly, both Shira and John were present at this meeting– it probably means we’re expecting progress 😀

Eddie Ma

July 22nd, 2009 at 5:36 pm

Zinc, the Entertainment Unit

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Firefox Eats Cara's TV

Firefox Eats Cara's TV

Way back at the beginning of this month, I sent away to Apple to order a DVI-I to S-Video / RCA connector. The total cost was $35 after shipping and tax, so it was well worth it as now I’ve gotten yet more value out of the Mac Mini.

The circa 1980’s television set can now play all of the media that is on the network, on the internet or on whatever other storage you can plug into Zinc, the Mac Mini.


DVI-I to S-Video and RFA

DVI-I to S-Video and RCA

Technical Stuff about DVI Connectors

When looking for a DVI to RCA video connector, the wrong thing to do is to go to a big computer shop. These places will turn you away and tell you the part doesn’t exist. Heck, even the hobby shops failed to provide it or give any useful information. And you know– they’re half right. There’s no such thing as a DVI-D to RCA connector, because the former is a digital signal, and the latter is an analogue signal. The DVI-I is port is offers a combined digital and analogue signal, that’s how it can be converted out to such a large variety of display devices. It’s one of the selling points that Apple discusses about its laptops and other machines.

Buy it or not…

If you purchased a computer with a DVI-D output, you won’t be able to use Apple’s connector– so don’t try, you’ll waste your money and be frustrated– however, if you have a machine with DVI-I output, then this thing will work for you too even though big and small shops alike will tell you the connector doesn’t exist.


Simply Charming

I also got two charming flotation device / pillow / toys packaged with the connector!

Conclusion: I’m happy 😀

Eddie Ma

July 12th, 2009 at 4:25 pm

Monet Molecules c/o Autotrace

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A Monet Isopentenol c/o Autotrace

A Monet Isopentenol c/o Autotrace

Brief: Happy accidents make me happy– here’s isopentenol after grabbing it as an SDF out of PubChem, dumping it out into a PNG with Bioclipse, grayscaling it with GIMP— then converting it to an SVG with Autotrace (RO IT Systems)… It’s just pretty… like a Monet. Of course, I have to go back and make it look like a molecule again for a paper… but I’m going to admire the pretty little alcohol for a bit.

Eddie Ma

July 9th, 2009 at 2:56 pm

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NNcmk: A Neural Network (Win32 & OSX)

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Okay– I managed to finish that 3-layer neural network implementation the other day– actually, it was a while ago but I didn’t post about it from being busy. It’s a pretty standard network, but I’m proud to say it’s small and works for OSX and Win32. I have to put in a few #define directives to have it work with Linux as well.

I will have to document it too when I get a chance. The reason why I made a brand new executable (instead of using the source from my previous projects) is because I needed something that would take in launch-time parameters so that it didn’t need to be recompiled each time someone decides to use the binary on a new dataset with a different number of inputs. Right now, the thing has barely any solid parameters that can’t be touched at launch-time.

The NNcmk (Neural Network – Cameron, Ma, Kremer) package is C compilable, uses the previously developed in-house library for the NGN and will be available shortly after I’m satisfied that I’ve squashed all the bugs, fixed the output and have documented the thing completely. I think Chris has difficulty with it right now mostly because I didn’t specify exactly what parameters do what– I did at least provide a (DOS) batch file with an example run-in-train-mode / run-in-test-mode sequence…

Back to work on that paper right now though…