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OpenMKM v0.4 is released. This version comes with inbuilt sensitivity analysis capability. Check the folder PFR_with_sensitivity under examples. Add the sensitivity keyword and the reaction ids under sensitivity keyword to evaluate sensitivity coefficients corresponding to the selection reactions. Additionally bugs that are generating NaN in PFR modeling are fixed.
Data Types:
  • Software/Code
No description provided.
Data Types:
  • Software/Code
This repository contains genome annotation files for the genome assembly reported in Kapheim et al. 2020.
Data Types:
  • Other
  • Sequencing Data
  • Tabular Data
  • Dataset
Redesigning BlobTools to support interactive data exploration
Data Types:
  • Software/Code
Change in prerequisites C++11 is required. C++98 is not supported anymore. Support of boost and dSFMT for random number generator is removed. CMake (>= 3.6) is required. Change in the directory structure Public header files are moved into include/mptensor. Change in the interface Format of the file IO is changed to support save/load with a different number of processes. Bug Fix A bug in SVD of a complex tensor without calculating the singular vectors is fixed.
Data Types:
  • Software/Code
We report a method, ContamLD, for estimating autosomal ancient DNA (aDNA) contamination by measuring the breakdown of linkage disequilibrium in a sequenced individual due to the introduction of contaminant DNA, leveraging the idea that contaminants should have haplotypes uncorrelated to those of the studied individual. Using simulated data, we confirm that ContamLD accurately infers contamination rates with low standard errors (e.g. less than 1.5% standard error in cases with <10% contamination and data from at least 500,000 sequences covering SNPs). This method is optimized for application to aDNA, leveraging characteristic aDNA damage patterns to provide calibrated contamination estimates. Availability: https://github.com/nathan-nakatsuka/ContamLD.
Data Types:
  • Software/Code
We are preserving the exact Conda computing environment used for the `EIA Cleaned Hourly Electricity Demand Data` project. See the resulting data and the code used to clean the data. This Conda environment `data_cleaning_env_OSX_10.14.tar.gz` was created using Mac OSX 10.14.6 and is only expected to run on recent versions of Mac OSX. A list of the included packages can be found in the `package-list.txt` file. To install this Conda environment once Conda is already installed and this archive is downloaded and unzipped: mkdir data_cleaning_env tar -xzf data_cleaning_env_OSX_10.14.tar.gz -C data_cleaning_env source data_cleaning_env/bin/activate conda-unpack
Data Types:
  • Software/Code
The main GKBS UI for the new DB titled cropbase_v5. The database is currently being updated by the interns, therefore tables and fields might change during this time. The final UI will be uploaded once every data migration and upload has been completed.
Data Types:
  • Software/Code
release to initiate doi creation with Zenodo
Data Types:
  • Software/Code
Added ModelTSO class and some bug fixes.
Data Types:
  • Software/Code
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