Overview
TeselaGen's TEST module provides a solution that extends the database concept by offering a graphical interface and tools that allow managing, sharing, visualizing and analyzing biological data. TEST is focused on tasks that have an increasingly important role in the synthetic biology field where companies are facing great challenges such as computer-aided design, manufacturing, project management, data acquisition and analysis. These companies are also confronting the data-dispersal problem: valuable data is produced by a wide range of devices in the laboratory, making it difficult to store them in an organized and coherent manner.
TeselaGen develops powerful software based on cloud technologies focused on computer aided design which considers the Design-Build-Test-Learn cycle (D-B-T-L). The TEST module is based on the Experimental Data Depot (EDD) solution, a bioinformatic open-source software and an experimental biological data and metadata repository developed by Lawrence Berkeley National Lab (LBNL) and Sandia National Lab (SNL) that enriches certain aspects of the D-B-T-L cycle of bio-manufacturing.
The TEST module is developed as a web tool that broadens the database concept allowing the capture of valuable data. The TEST module was designed to support different use cases and types of experimental data from synthetic biology laboratories. In addition, TEST helps structure and standardize data from experimental results that can be used to train machine learning models in TeselaGen’s DISCOVER module.
Main features
Upload, export, manage, share, transport and display biological data through an intuitive graphical interface.
Structure and standardize data from experimental results. In addition to capturing valuable information, this module can be used to feed machine learning models in TeselaGen’s DISCOVER module. This allows you to complete the D-B-T-L cycle by providing predictions that enrich the optimization of the experimental work.
More about what you might be interested in
Interactive Data Visualization
Our TEST app provides visualization of experimental data through interactive
tables and graphs. Visualization gives the researcher a quick data quality check by testing whether the gathered data matches intuitive expectations.
Data Standardization
The Test app provides a single repository of data and a set of unified workflows for data input which facilitate standardized data collection and storage. This standardization facilitates comparison of experiments accumulated over time and provides a unified input for data analysis. The Test app provides access to all the data pertaining to an experiment in the form of standardized output files and a RESTful API in order to access data programmatically. Two output formats are provided at this time: comma separated values (CSV) and SBML.
Database Schema
The Test App (EDD) can uptake experimental data, provide visualization of these data, and produce downloadable data in several standard output formats. The Test App (EDD) is not a LIMS (Laboratory Information Management System): it is not meant to store raw data (e.g., mass spectrometry traces). Rather, it only stores processed biologically interpretable data (e.g., metabolite concentrations, protein expression levels, oxygen input rates, etc.). For accurate understanding check out this glossary.
Architecture
The Test App (EDD) code is a branch from the open source under a Berkeley Software Distribution (BSD) license. The front-end of EDD is written in TypeScript, JavaScript, and HTML/CSS. The backend is coded in Python and built on the Django platform. Database is PostgreSQL.