DSKernel: AI and Strength Training

At GYDLE inc., I work on optical mapping problems, and sometimes I find solutions to these problems. To tackle efficiently any problem, the error model for the problem must be understood. To write software that deals well with a given type of data, this type of data has to be understood, and one must be able to separate the good data from the bad data. Once in a while, I read scientific papers to keep myself up to date with the optical mapping technologies. I created a Mendeley group where I maintain a list of papers on optical mapping. The list is available here . Some of these papers describe error models for optical mapping.

According to  the social network LinkedIn, I have been working on optical mapping problems at Gydle Inc. (with Philippe and Marc-Alexandre) for 8 months so far. I previously worked at Argonne National Laboratory (with Fangfang and Rick and other people). The Bioinformatics Adventure continues. Yes, I am still doing bioinformatics. No, I no longer work on assemblers. I have not worked on any genome assemblers for a while. As of now, I am more an aligner person than an assembler person (see " Sense from sequence reads: methods for alignment and assembly "). At Gydle Inc, we are 3 employees (the CEO, a computer scientist, and myself). Our CEO worked at Illumina at some point. Working in a small company is very fun. We get to do a lot of different things: algorithm design, software design, software development, software quality control, test development, ticket management, data analysis, data curation. I schedule my time around activities related to the develo...

I received my Spark Notebook. What is the Spark Notebook, you may ask. The Spark Notebook combines form and function. The Spark Notebook project raised funding on Kickstarter too. The way I see it, the Spark Notebook is an agenda (a 6-month agenda) with additional features. These features include (from the guide ) the yearly planning pages, accomplishments, the monthly planning pages, the weekly planning pages, the inspiration pages, and the note pages. The monthly planning pages include something called the 30-day challenge. According to creator Kate Matsudaira, the 30-day challenge feature is useful to help start (or break) a habit . The Spark Notebook comes with a guide . On this website, some of the text is white with a background image which makes it hard to read. For example, consider the screenshot below. How did I learn about the existence of the Spark Notebook ? One of my hobbies consists in watching videos on the Amazon Web Services (AWS) YouTube channel. I...

An exascale computer is an imaginary system that can sustain one exaflops (10^18 floating point operations per second.) Such an object is needed in science and engineering, mostly for simulating virtual versions of objects found in the real world, such as proteins, planes, and cities. Important requirements for such a computer are 1) memory bandwidth, 2) floating point operation throughput, 3) low network latency, and so on. 2 of the many challenges for possibly having exascale supercomputers by 2020 are 1) improving fault-tolerance and 2) lowering energy consumption. (see " No Exascale for You! " An Interview with Berkeley Lab's Horst Simon). One typical solution to implement fault tolerance in HPC is the use of the checkpoint/restart cycle whereas in most cloud technologies fault tolerance is instead implemented using different principles/abstractions such as load balancing and replication (see the CAP theorem ). The checkpoint/restart can not work at the exa scale...

Thorium is an actor model engine in C 1999. It uses MPI and Pthreads. The latency (in Thorium) when sending small messages between actors recently came to my attention. In this post, LTTng-UST is used to generate actor message delivery paths annotated with time deltas in each step. Perf I have been working with perf for a while now, but found it only useful mostly for hardware counters. I typically use the following command to record events with perf. Note that ($thread is the Linux LWP (lightweight process) thread number. perf record -g \     -e cache-references,cache-misses,cpu-cycles,ref-cycles,instructions,branch-instructions,branch-misses \     -t $thread -o $thread.perf.data     As far as I know, perf can not trace things like message delivery paths in userspace. Tracing with LTTng-UST   This week, I started to read about tracepoints (perf does support "Tracepoint Events"). In particular, I wanted to use tracepoints t...

I am currently in an improvement phase where I break, build and improve various components of the system. The usual way of doing things is to have a static view of one node among all the nodes inside an actor computation. The graphs look like this: 512x16 1024x16 1536x16 2048x16 But with 2048 nodes, the one single selected node may not be an accurate representation of what is going on. This is why, using Thorium profiles, we are generating 3D graphs instead. They look like this: 512x16 1024x16 1536x16 2048x16

I am working on a couple of very large public metagenomics datasets from the Department of Energy (DOE) Joint Genome Institute (JGI). These datasets were produced in the context of the Grand Challenge program. Professor Janet Jansson was the Principal Investigator for the proposal named Great Prairie Soil Metagenome Grand Challenge ( Proposal ID: 949 ). Professor C. Titus Brown wrote a blog article about this Grand Challenge . Moreover, the Brown research group published at least one paper using these Grand Challenge datasets ( assembly with digital normalization and partitioning ). Professor James Tiedje presented the Great Challenge at the 2012 Metagenomics Workshop. Alex Copeland presented interesting work at Sequencing, Finishing and Analysis in the Future (SFAF) in 2012 related to this Grand Challenge. Jansson 's Grand Challenge included 12 projects . Below I made a list with colors (one color for the sample site and one for t...