A software that infers the tumor purity and ploidy from a pair of tumor-normal whole-genome sequencing data. It differentiates from others by performing well in low-purity and low-coverage samples.
Check the Accurity page for more details.
To access the bioinformatics data generated in the 个性化药物先导专项, please login https://bioinfo.simm.ac.cn/. It contains >100TB NGS genomics, transcriptomics, histo-imaging, and proteomics data, generated during the drug development pipeline.
PatientStratifier is a software package that stratifies patients based on patient biomarker data and drug response data. Its core is a machine learning module that learns from existing patient biomarker and drug response data. It also has a component called PatientRecommender that recommends if a patient should be given a drug or not based on its biomarker data.
A workflow that analyzes ~900 genomes (cumulative coverage ~4000). Starting from billions of 100bp paired-end reads by Illumina GenomeAnalyzer II, the whole workflow is comprised of several different sub-workflows: the read filtering sub-workflow (whose main program is a custom-written java program based on GATK libraries), the read alignment sub-workflow (main program is bwa [Li et al. 2009], stampy[Lunter et al. 2011] used in test), the base-quality-score-recalibration sub-workflow by GATK [DePristo et al. 2011], the genotype-calling sub-workflow by SAMtools [Li et al. 2009] and GATK [DePristo et al. 2011], the pedigree calling sub-workflow (main program is TrioCaller [Chen et al. 2012]), and other sub-workflows that carry out the variant-filtering and statistics-calculation (Transition/Transversion, allele-frequency, Mendelian inconsistency, population genetic measures such as nucleotide diversity, Hardy-Weinberg equilibrium p-value, linkage disequilibrium). All workflows interact with the vervet postgreSQL database seamlessly through sqlalchemy/elixir. The workflows were constructed in a MapReduce manner using APIs from the Pegasus workflow management system to take full advantage of the parallel computing power in most clusters. The end-result is a powerful and flexible system that is capable of utilizing the full power of a computing cluster. The main code could be found at http://code.google.com/p/vervet-web/. Substantial java and C++ code are in private git repositories (contact polyactis@gmail.com if interested).
This is a job-dependency DAG (direct acyclic graph).
This is the job-duration vs. time diagram, illustrating which job takes most time, from a toy example. The real-data workflows involve 100X or more jobs.
The most update URL is at http://arabidopsis.gmi.oeaw.ac.at:5000/ (old links from http://arabidopsis.usc.edu/ will be re-directed to this GMI site). The MySQL database dump could be downloaded from http://arabidopsis.gmi.oeaw.ac.at/public_db_dump.tar.gz. All the code for the version demonstrated in Huang et al. 2011 could be found in this tarball (Pylons web server, web client using Google web toolkit, etc.).
A second-generation version is at http://gwas.gmi.oeaw.ac.at/index.html (Seren et al. 2012, source code link). The Arabidopsis polymorphism effort is at https://cynin.gmi.oeaw.ac.at/home/resources/atpolydb.