The LCSB LUX team (me, Enrico, and Roland) just published an official supplementary page for the Single Cell Transcriptomics DREAM Challenge:
(EDIT): Preprint is available at medrxiv
Btw. we ranked 10-13 out of 34 teams (not bad I guess).
My seemingly random thoughts
The LCSB LUX team (me, Enrico, and Roland) just published an official supplementary page for the Single Cell Transcriptomics DREAM Challenge:
(EDIT): Preprint is available at medrxiv
Btw. we ranked 10-13 out of 34 teams (not bad I guess).
The first official public release of Ada Discovery Analytics -version 0.7.3- with two installation guides (Linux/Ubuntu and MacOS) is out:
https://github.com/ada-discovery/ada-web/releases/tag/v0.7.3
Working tirelessly now on the next release (0.8.0), which will introduce several key improvements, especially for the persistence layer.
Our paper titled “Shift-symmetric Configurations in Two-dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration” got published in Chaos!
https://aip.scitation.org/doi/10.1063/1.5089889
Hoping for a revival of the cellular automata field.
To better explain the enumeration and probability calculation part of our paper “Shift-Symmetric Configurations in Two-Dimensional Cellular Automata: Irreversibility, Insolvability, and Enumeration,” which is currently under preparation (preprint available here), I’ve created a little supplementary web page and added it to COEL project as a new Symmetry section:
It’s freely accessible so go ahead and give it a try!
I’m happy to announce that Apr 28th COEL framework became open-source as defined by the standard Apache Licence 2.0.
Check out the code at https://github.com/peterbanda/coel. If you want to contribute to the project contact me at mail@peterbanda.net
.
Giving two talks this week at ALIFE 14 conference at the Artificial Chemistry session and the CoSMoS workshop. The papers available here and here.
Our paper titled “Learning Two-input Linear and Nonlinear Analog Functions with a Simple Chemical System” has been accepted to Unconventional Computing & Natural Computing 2014 conference which will be held in London, Ontario this summer. Check out a preprint of our paper here.
Our work on chemical learning was featured in a recent article published at Chemistry World by renowned science writer Philip Ball.
Our papers referenced in the article are:
P. Banda, C. Teuscher and M. R. Lakin, Artif. Life, 2013, 19, 195 (DOI: 10.1162/artl_a_00105)
P. Banda, C. Teuscher and D. Stefanovic, J. R. Soc. Interface, 2014, DOI: 10.1098/rsif.2013.1100
Thanks to a GridGain academic licence the COEL framework enjoyes a scalable zero-deployment computational grid, which flawlessly fits to our Spring-backed IoC container. The grid can employ up to 512 cores to run mainly chemical simulations, dynamics analyses, and evolutionary optimizations of rate constants.
In Sept ’13 GridGain and PSU released a short press statement (260 pick-ups) describing our colaboration:
prnewswire.com, bio-medicine.org, hpcwire.com
Recently I was trying to set up a MySQL database for one of my projects. The major difficulty I’ve faced is that MySQL apparantly does not provide any support for Linux (user-defined) variables… or maybe I’m just lame since I was not able to find that. So after I’ve spent a couple of hours browsing and cursing, I decided to write a bash script that parses a given SQL file, replaces (evaluates) all ${..} ocurrences with the values of Linux variables, and finally runs the adjusted SQL.
It worked well on Ubuntu 11.10 with MySQL 5.1.63.
If you want to use it replace the assigments of all DB variables such as DB_HOST
and DB_USER
in the following bash script (create_DB.sh
) with your own setting.
#!/bin/bash # The name of the script SCRIPT_NAME=create_DB.sql # Variables DB_HOST=localhost DB_PORT=3306 DB_ADMIN=root DB_USER=dbadmin DB_USER_PASSWORD=xxxx DB_NAME=db # Collect variables and substitute for var in `grep -o "\\$*{\([^{]*\)}" $SCRIPT_NAME` do val=`eval echo ${var}` vars+=("-e s/$var/$val/g") done # Run the SQL script sed "${vars[@]}" $SCRIPT_NAME | sudo -u $DB_ADMIN mysql -v -p -h $DB_HOST -P $DB_PORT
Here is the referenced MySQL script (create_DB.sql
):
-- CREATE USER CREATE USER '${DB_USER}'@'%' IDENTIFIED BY '${DB_USER_PASSWORD}';</code> -- CREATE DB CREATE DATABASE IF NOT EXISTS ${DB_NAME} CHARACTER SET utf8; -- GRANT PRIVILEDGES GRANT ALL PRIVILEGES ON ${DB_NAME}.* TO '${DB_USER}'@'%' WITH GRANT OPTION;
eNjOY!