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ImmuneDB — ImmuneDB 0.19.x documentation

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Is a system that facilitate efficient storage and analysis of high-throughput B- and T-cell sequence data. It provides V- and J-gene identification, clonal assignment, lineage construction, selection pressure calculation, and thorough exporting functionality. ImmuneDB is comprised of two code bases: Python analysis tools ( GitHub. And a web interface ( GitHub.

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ImmuneDB — ImmuneDB 0.19.x documentation | immunedb.com Reviews

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Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Is a system that facilitate efficient storage and analysis of high-throughput B- and T-cell sequence data. It provides V- and J-gene identification, clonal assignment, lineage construction, selection pressure calculation, and thorough exporting functionality. ImmuneDB is comprised of two code bases: Python analysis tools ( GitHub. And a web interface ( GitHub.

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ImmuneDB — ImmuneDB 0.19.x documentation | immunedb.com Reviews

https://immunedb.com

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Is a system that facilitate efficient storage and analysis of high-throughput B- and T-cell sequence data. It provides V- and J-gene identification, clonal assignment, lineage construction, selection pressure calculation, and thorough exporting functionality. ImmuneDB is comprised of two code bases: Python analysis tools ( GitHub. And a web interface ( GitHub.

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immunedb.com

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ImmuneDB

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Directly Querying the Database — ImmuneDB 0.19.x documentation

http://immunedb.com/database.html

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Directly Querying the Database. Directly Querying the Database. ImmuneDB is backed by a MySQL database that can be queried directly to gather information, bypassing the Python API. There are many ways to access the database directly. The two introduced here are directly through MySQL or using. Which simply wraps a call to MySQL. Mysql -u USERNAME -p DATABASE.

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Common Classes & Functions — immunedb.common — ImmuneDB 0.19.x documentation

http://immunedb.com/common.html

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Common Classes and Functions —. Common Classes and Functions —. Module provides methods to initialize a connection to a new or existing database. Most programs using ImmuneDB will start with code similar to:. Get base arg parser. Some description of the program. Add any additional arguments to the parser . To avoid using a configuration file, the. All will return a.

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Data Analysis Pipeline — ImmuneDB 0.19.x documentation

http://immunedb.com/pipeline.html

Getting Started (Docker Compose). Getting Started (Bare Metal). Local Alignment of Indel Sequences (Optional). Directly Querying the Database. Common Classes and Functions —. Data Models —. The primary component of ImmuneDB is its clonal identification pipeline which has the capability to take as input raw sequences, determine likely V and J genes, and finally group similar sequences into clones. Immunedb admin create DB NAME CONFIG DIR. With an appropriate database name and. After running this, a databa...

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Python Module Index — ImmuneDB 0.19.x documentation

http://immunedb.com/py-modindex.html

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Immunedb.api.rest service. Provided by Read the Docs.

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simlab.biomed.drexel.edu

Systems Immunology Lab: Publications

http://simlab.biomed.drexel.edu/publications.php

Melunis, J, Hershberg, U. (2016) A spatially heterogeneous Gillespie algorithm modeling framework that enables individual molecule history and tracking. Engineering Applications of Artificial Intelligence (In press) PDF. BMC Bioinformatics, 17, 333. PDF. Rosenfeld, am, Meng, W., Luning Prak, E.T., Hershberg, U. (2016) ImmuneDB: A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. Journal of Immunology 196, pp 209. Retrovirology 13, 1 14. PDF. Winter, M&#4...

rosenfeld.io

Aaron M. Rosenfeld | Home

http://www.rosenfeld.io/home

Aaron M. Rosenfeld. This is the personal and professional website of Aaron Rosenfeld. I graduated from Drexel University with a Master's degree in Computer Science and currently hold a Bioinformatics Software Engineer and Lab Manager position with the school's Systems Immunology Lab. 2016, Oxford Journal of Bioinformatics. ImmuneDB: A system for the analysis and exploration of high-throughput adaptive immune receptor sequencing data. 2016, BMC Bioinformatics. 2016, Bioinformatics Open Source Conference.

rosenfeld.io

Aaron M. Rosenfeld | Projects

http://www.rosenfeld.io/projects

Aaron M. Rosenfeld. ImmuneDB 2014 – present. ImmuneDB is a Python system for the processing of IGHV sequencing data including V- and J-gene identification, clonal assignment, mutation analysis, and lineage construction. It is implemented as a suite of command line tools, uses MySQL to store all information, and provides a web interface, implemented in React, for visualization. Transport Engine 2012 – 2014. Ahoy 2010 – 2011. PhpWatch 2008 – present. I am the lead developer of phpWatch, a free, open-source...

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ImmuneDB — ImmuneDB 0.19.x documentation

Getting Started (Docker Compose). Getting Started (Bare Metal). Directly Querying the Database. Common Classes and Functions —. Data Models —. Is a system that facilitate efficient storage and analysis of high-throughput B- and T-cell sequence data. It provides V- and J-gene identification, clonal assignment, lineage construction, selection pressure calculation, and thorough exporting functionality. ImmuneDB is comprised of two code bases: Python analysis tools ( GitHub. And a web interface ( GitHub.

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