7 Works

MatLab tools for estimating linear Fisher information from population data along with synthetic data and recorded spike count responses from neurons in macaque primary visual cortex to grating images with different orientations and white noise.

Ingmar Kanitscheider, Ruben Coen-Cagli, Adam Kohn & Alexandre Pouget
This package contains some MatLab tools for estimating linear Fisher information from population data. Also included are two datasets (one synthetic, including the ground truth information; and one recorded in macaque primary visual cortex) to test the code. The code and the data sets are described in the associated paper: Ingmar Kanitscheider, Ruben Coen-Cagli, Adam Kohn, Alexandre Pouget "Measuring Fisher information accurately in correlated neural populations". PLoS Comp. Biol. 2015

MatLab tools for building Mixture of Gaussian Scale Mixture (MGSM) models, and perform inference and learning.

Ruben Coen-Cagli, Peter Dayan &
This package contains some MatLab tools for building Mixture of Gaussian Scale Mixture (MGSM) models, and perform inference and learning. MGSM models, and their application to the statistics of natural images and contextual phenomena in the visual cortex, are describe in the associated paper: Coen-Cagli, Dayan, Schwartz. "Cortical Surround Interactions and Perceptual Salience via Natural Scene Statistics". PLoS Comp Biol 2012. DOI: 10.1371/journal.pcbi.1002405

The Evolution of Function within the Nudix Superfamily: generate score script

John Srouji, Anting Xu, Annsea Park, Jack Kirsch & Steven Brenner
The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205...

Sino-Tibetan Etymological Dictionary and Thesaurus Database Software

Daniel Bruhn, John Lowe, David Mortensen & Dominic Yu
several software suites which support access to the STEDT database. These are written in PERL and PHP, and present different capabilities and dimensions of this linguistic data. This object is a compressed archive of the svn code repository for the project as of January 5, 2015. The active repository is now on GitHub at https://github.com/stedt-project/sss.

Toolkit for Extreme Climate Analysis

The Evolution of Function within the Nudix Superfamily: Python script

John Srouji, Anting Xu, Annsea Park, Jack Kirsch & Steven Brenner
The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205...

The Evolution of Function within the Nudix Superfamily: generate final score script

John Srouji, Anting Xu, Annsea Park, Jack Kirsch & Steven Brenner
The Nudix superfamily encompasses over 80,000 protein domains from all three domains of life. These proteins fall into four general functional classes: isopentenyl diphosphate isomerases (IDIs), adenine/guanine mismatch-specific adenine glycosylases (A/G-specific adenine glycosylases), pyrophosphohydrolases, and non-enzymatic activities such as protein/protein interaction and transcriptional regulation. The largest group, pyrophosphohydrolases, encompasses more than 100 distinct hydrolase specificities. To understand the evolution of this vast number of activities, we assembled and analyzed experimental and structural data for 205...

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