(or, What I Did For One Day Of My Summer Vacation.)
tl;dr? I played around with building a CountMin Sketch that is dynamic in size, based on a scalable Bloom Filter approach. I'm not sure it worked. Thoughts, suggestions, help?
In our research, we've made some hay …
There are comments.
About 10 days ago, I gave a talk in Manchester to Carole Goble's group, hosted by Aleksandra Pawlik. The talk title was "Six ways to Sunday: Approaches to computational reproducibility in non-model sequence analysis." I've posted the slides (here).
For the talk, I put together a list of five things …
read moreThere are comments.
I'm on a European trip that involves several plane flights accompanied by long airport stays, and I just used some of that time to do a bit of tedious coding on khmer.
The coding I did was to add proper exception handling to khmer's internal file loading routines (see the …
read moreThere are comments.
Earlier today, I posted our response to the reviewers' comments on our k-mer counting paper, "These are not the k-mers you are looking for: efficient online k-mer counting using a probabilistic data structure.
A side note -- I was wondering how many public examples there are of the whole paper submission …
read moreThere are comments.
A few months back, we received some reviews for our paper on k-mer counting with khmer. After many months, we (mostly Qingpeng Zhang, the first author) has finished revising the paper. Here is our response to reviewers.
The latest (resubmitted) version of the paper is here, while the version the …
read moreThere are comments.
I've just made my full application to the Moore Foundation's Data Driven Discovery Investigator program available, but wanted to post an HTML version, too. You can also see a short sci-fi story about what I want to enable.
You might wonder why I'm posting this. Well, there's a snowflakes chance …
read moreThere are comments.
My second-round Data Driven Discovery application is due on Monday, and my first draft contained the following story. I don't think I'll include it in the actual application, but it was entertaining enough to write that I thought I'd post it here.
A vision of the future I would like …
read moreThere are comments.