biosoc.org

About us ✍

BioSoc Society hopes to empower all community members to be makers and creators rather than passive recipients. Everyone is encouraged to contribute, no matter what skill level. We support over a dozen applications in the synthetic biology community and many on Github. Contributions require testing, bug reports, user documentation, and code examples.

BioSoc Software ✍

✍

List

CAD Tools

graph TD
    A[Synthetic Biology Software Tools]
    
    A --> B[CAD Tools]
    B --> B1[SBOLDesigner: genetic constructs]
    B --> B2[3DμF: microfluidic device design]
    B --> B3[Primer3: design for PCR and sequencing]

SBOLDesigner

A biologist-friendly computer-aided design (CAD) software tool for creating and manipulating genetic constructs using the SBOL 2.2 data model.

3DμF

A visual CAD tool for designing microfluidic devices with outputs in STL, SVG, and JSON formats.

Primer3

Tool for designing and analyzing primers for PCR reactions, sequencing reactions, and hybridization probes.

Microfluidic Automation

graph TD
    A[Synthetic Biology Software Tools]
    
    A --> C[Microfluidic Automation]
    C --> C1[PyHamilton: Libraries for Hamilton liquid handling robots]
    C --> C2[Fluigi: Automates microfluidic device design]

PyHamilton

A library for standardized operations with Hamilton liquid handling robots.

Fluigi

Automates the design of microfluidic devices using the MINT language.

Data Management

graph TD
    A[Synthetic Biology Software Tools]
    
    A --> D[Data Management]
    D --> D1[Clotho: synthetic bio systems and data framework]
    D --> D2[Knox: genetic design spaces repository]
    D --> D3[OWL: synthetic biology generator]

Clotho

Framework for engineering synthetic biological systems and managing the associated data, supporting schema authoring and function execution.

Knox

Web-enabled repository for storing, modifying, and tracking genetic design spaces as directed graphs.

OWL

Datasheet generator for synthetic biology, facilitating efficient datasheet creation and management.

Analysis Tools

graph TD
    A[Synthetic Biology Software Tools]
    
    A --> E[Analysis Tools]
    E --> E1[BioConductor: Analysis using R language]
    E --> E2[Copasi: Simulates biological systems with ODEs & SBML]
    E --> E3[RoadRunner: Portable simulation for SBML models]
    E --> E4[Morpheus: Cell-based modeling environment]

BioConductor

Analysis and comprehension tool using the open-source statistical language, R.

Copasi

Simulates biological systems using ODEs and the Gillespie stochastic simulation algorithm, supporting SBML models.

RoadRunner

Portable simulation engine for systems and synthetic biology models in SBML format.

Morpheus

Modeling environment for simulating cell-based models with ordinary differential equations and reaction–diffusion systems.

Synthetic Biology Standards, Languages, Libraries

graph TD
    A[Synthetic Biology Software Tools]
    
    A --> F[Synthetic Biology Standards, Languages, Libraries]
    F --> F1[Antimony: Modular language for model definitions]
    F --> F2[CELLO: Genetic circuit design via Verilog]
    F --> F3[Eugene: Rule-based design for bio systems]
    F --> F4[GSL: Design language for complex DNA constructs]

Antimony

A modular human-readable/writable model definition language with easy translation into SBML.

CELLO

Software for creating genetic circuits based on high-level logic specifications in Verilog.

Eugene

Language ecosystem for rule-based design of synthetic biological systems, devices, parts, and DNA sequences.

GSL

Language for designing complex DNA constructs used to engineer genomes.

BiologyTools

Design tools ✍

This README provides a structured overview of various software tools developed by cidarlab.org, genedesign.org, hicsail, salislab, synbiohub.org, and others focusing on those for designing synthetic biology constructs. Each tool has its specific use cases, features, and resources available for further exploration.

Parses a rich set of operators as defined by GOLDBAR and enumerates genetic designs that satisfy user-defined specifications through mathematically rigorous graphs.

SBOL Designer

SBOLDesigner is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2.2 data model.

SBOL is an open standard for the representation of in silico biological designs, and the icons used in this tool are provided by SBOL Visual. Design spaces are expressed in SBOL via the CombinatorialDerivation extension and can be exported and stored in Knox. This third form of design space representation allows Constellation to be easily integrated in the synthetic biology community.

Key Features

SBOLDesigner is a user-friendly computer-aided design (CAD) software tool specifically designed for biologists. It allows users to create and manipulate genetic construct sequences using the Synthetic Biology Open Language (SBOL) 2.2 data model. With SBOLDesigner, researchers can efficiently design and analyze genetic constructs for synthetic biology projects.

  1. Biologist-Friendly Interface: SBOLDesigner is designed with biologists in mind. Its user-friendly interface makes it accessible to researchers who may not have extensive computational or programming experience.

  2. SBOL 2.2 Support: The software adheres to the Synthetic Biology Open Language (SBOL) 2.2 data model. This standard allows users to represent genetic constructs, parts, and sequences in a consistent and interoperable format.

  3. Construct Design and Manipulation: SBOLDesigner enables users to create, edit, and manipulate genetic constructs. You can assemble DNA parts, specify their sequences, and organize them into functional units.

  4. Visual Representation: The tool provides visual representations of genetic constructs, making it easier to understand and communicate complex designs. Graphical views help users visualize the arrangement of parts and their interactions.

  5. Annotations and Metadata: SBOLDesigner allows users to annotate constructs with additional information, such as functional descriptions, provenance, and experimental data. Metadata enhances the documentation and traceability of designs.

  6. Export Options: You can export your designs in SBOL format for sharing with other tools or collaborators. This interoperability ensures seamless integration with other software in the synthetic biology workflow.

Resources

constellation-js

Library for combinatorially specifying, constraining, and exploring genetic design spaces.

Resources

GeneDesign

Web-based synthetic gene designer with various modules for sequence manipulation such as reverse translator and codon juggler.

Resources

Pigeon

Web-based tool for translating a textual description of a synthetic biology design into an image, allowing for the programmatic generation of design visualizations.

Resources

Raven

Uses a dynamic programming algorithm to design high-quality DNA assembly plans and produces SBOL-compliant images with human-readable instructions.

Resources

TASBE

Synthetic biology automation software for tasks from high-level specification to part assignment and assembly.

Resources

DAFD

First microfluidic design automation software that uses machine learning to deliver a user-specified desired performance.

Resources

Mage

Java part of MERLIN for analyzing genetic packages.

Resources

Puppeteer

Web-based planning and instruction generation tool for automating DNA assembly tasks, translating protocols into human- and machine-readable instructions.

Resources

Sequence Refiner

Sequence alignment tool that refines a multiple sequence alignment by iterative realignment with a predetermined conserved core model of a protein family.

Resources

Vector Editor

Web-based DNA sequence-editing and analysis tool with features like restriction enzyme manager, amino acid translation, and gel digest prediction.

Resources

Double Dutch

Tool for designing combinational libraries of biological systems using response surface methodology.

Resources

Phoenix

Framework for designing complex genetic systems focusing on behavior over time rather than steady-state behavior.

Resources

RBS Calculator

Predicts and controls translation initiation and protein expression, also optimizes synthetic RBS sequences to achieve targeted translation initiation rates.

Resources

SynBioHub

Design repository for uploading and sharing DNA and protein designs.

Resources

iBioSim

Tool for modeling, analysis, and design of genetic circuits, also applicable to other biological and chemical systems.

Resources

Analysis Software ✍

various computational biology software tools, including their types, functionalities, and access to their project websites, source codes, and demos.

AnalysisTools

Aquarium

Analysis and comprehension tool leveraging the open-source statistical language, R. AMI and Docker images are available.

Resources

Copasi

A standalone program supporting SBML standard models, capable of simulating behavior using ODEs or the Gillespie stochastic simulation algorithm. It includes arbitrary discrete events in simulations.

Resources

Road Runner

A portable simulation engine for systems and synthetic biology models in SBML format. Written in C#, it incorporates C, C++, and Python APIs.

Resources

BioConductor

Analysis and comprehension tool using the open-source statistical language, R. AMI and Docker images are available.

Resources

Morpheus

A modeling environment for simulating cell-based models with ordinary differential equations and reaction–diffusion systems. It supports multiscale biological models defined in biological terms and mathematical expressions.

Resources

Tinkercell

Incorporates a detailed diagram that can be mapped to models or experimental results, allowing various mathematical analyses to be run on those models.

Resources

BioPSy

Performs guaranteed parameter set synthesis for ODE biological models expressed in SBML based on desired behavior expressed by time-series data.

Resources

Pysces

Provides tools for analyzing cellular systems, including a human-readable model description language, a structural, and a bifurcation analysis module. Supports SBML and SED-ML.

Resources

gro

A programming, modeling, specifying, and simulating language for the behavior of cells in growing microcolonies of microorganisms.

Resources

Software for Microfluidic and Biological Automation ✍

This repository provides a comprehensive list of tools designed to facilitate the design and automation of microfluidic devices and other biological tasks. Each tool comes with a description, relevant links to project websites, source code, and demo videos. Feel free to explore the links provided for more information and access to each software tool. For any additional inquiries or support, refer to the respective project websites and repositories.

CADTools

Contents

  1. 3DμF
  2. PyHamilton
  3. Fluigi
  4. Primer3

3DμF

3DμF is a visual CAD tool for designing microfluidic devices. It offers outputs in STL for CNC milling, SVG for lithography, and also provides a textual JSON representation.

PyHamilton

PyHamilton provides a set of standardized libraries developed for use with Hamilton liquid handling robots.

Resources

Fluigi

Fluigi automates the design of microfluidic devices used in synthetic biology by optimizing their layout based on specifications in the text-based MINT language.

Resources

Primer3

Primer3 is a tool used for designing and analyzing primers for PCR reactions. It also allows for the selection of primers for sequencing reactions and hybridization probes.

Resources

Data Management ✍

Comprehensive tools aimed at improving data management in synthetic biology. Each application offers specialized functionalities to support and enhance your research endeavors. For more information and to access the resources, please refer to the links provided. Should you have any questions or require further assistance, do not hesitate to contact us or visit our project repositories.

DataManagement

Clotho

Clotho is a versatile framework for engineering synthetic biological systems and managing the data associated with their creation. It allows users to author data schemas, execute functions and algorithms, and integrate with pre-existing applications seamlessly.

Resources

Knox

Knox is a web-enabled repository designed for the storage, modification, and tracking of genetic design spaces. It manages thousands of genetic design variants and represents them as directed graphs. Knox can be accessed via domains in the format <insertname>.knoxcad.org.

Resources

OWL

OWL is an automatic datasheet generator specifically designed for synthetic biology, facilitating efficient datasheet creation and management.

Resources

Synthetic Biology standards, languages, libraries ✍

This documentation provides a comprehensive overview of various software tools useful for synthetic biology applications. These tools cover a range of purposes including modular model definition, flow cytometry data analysis, genetic circuit creation, metabolic pathway mapping, genomic reprogramming, and DNA sequence generation.

Contents

  1. Antimony
  2. FloCal
  3. Kera
  4. CELLO
  5. GLAMM
  6. Merlin
  7. Eugene
  8. GSL
  9. MoSec

Antimony

A text-based modular human-readable/writable model definition language with capabilities of easy translation into SMBL.

Resources

FloCal

A library for reading, analyzing, and calibrating flow cytometry data; accepts FCS files as input and is compatible with different calibration particles, fluorescent probes, and cell types.

Resources

Kera

An object-oriented programming language for synthetic biology, tempered by the biopart rule library, Samhita.

Resources

CELLO

Software for creating genetic circuits, using as input a high-level logic specification written in Verilog.

Resources

GLAMM

Provides maps for metabolic pathways, biosynthesis of secondary metabolites, and microbial metabolism.

Resources

Merlin

A web-based application for genomic reprogramming via a rapid and efficient method known as Multiplex Automated Genome Engineering (MAGE).

Resources

Eugene

An ecosystem of languages tailored for rule-based design of synthetic biological systems, devices, parts, and DNA sequences.

Resources

GSL

A language that facilitates the design of large and complex DNA constructs used to engineer genomes; incorporates a set of low-level DNA manipulation primitives.

Resources

MoSec

Java application capable of generating DNA sequences, and exporting formats such as FASTA, GenBank, EMBL, and SBOL from SBML and CellML models.

Resources

This document provides a brief overview and resource links for synthetic biology tools to aid in various applications. For further information, visit the respective project websites and source code repositories.

Sources ✍

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