Critical components: Software for driving advances in synthetic biology
Software plays a transformative role in driving advances in synthetic biology. From designing biological systems and automating lab equipment, to managing collaborations and analyzing vast amounts of data, software underpins many of the essential tasks in making biology easier to engineer.
In honor of the 20th year of iGEM, we’d like to feature the Software developed by iGEM teams:
2006
Teams wrote their own software to aid in project design
Davidson 2006 (United States) created a dsDNA assembly program for gene synthesis from overlapping oligos.
Harvard 2006 (United States) wrote a program that can evolve a sequence for the linking region given two aptamer sequences.
2007
Software used or developed by iGEM teams featured on wikis as a resource for other teams
Calgary 2007 (Canada); Davidson Missouri W 2007 (United States); Imperial 2007 (United Kingdom); Melbourne 2007 (Australia); Valencia 2007 (Spain)
2008
Software Tools introduced as an experimental track within the iGEM Competition
UC Berkeley Tools 2008 (United States) developed “Clotho Classic”, a toolset designed in a platform-based design paradigm to consolidate multiple tools (sequence viewers/editors, parts database managers, assembly algorithm GUIs, etc.) into one working, integrated toolbox. Winner Best Software Tool, Gold Medal.
Teams featuring software on their wikis: BCCS-Bristol 2008 (United Kingdom); Bologna 2008 (Italy); Edinburgh 2008 (United Kingdom); iHKU 2008 (Hong Kong); KULeuven 2008 (Belgium); Minnesota 2008 (United States); Newcastle_University 2008 (United Kingdom); Tsinghua 2008 (China).
2009
Best Software Tool Winners (2009)
Berkeley Software 2009 (United States) Expanded the suite of software available to synthetic biologists to include “Eugene” - a domain specific language for the specification of biological constructs, “Spectacles” - a visual editing framework for the design of composite biological devices and the assignment of physical samples to functional concepts, and “Kepler Integration” - a development of actors and automated assembly processes for the scientific workflow management system Kepler. Winner Best Software Tool, Gold Medal.
Illinois-Tools 2009 (United States) developed Interactive Metabolic Pathway Tools (IMP Tools), an open source, web based program that involves model-guided cellular engineering where new metabolic functions can be added to existing microorganisms. Winner Best Software Tool, Gold Medal.
Teams in the Software Tools track (2009)
CBNU-Korea 2009 (Republic of Korea) Essarker: An Essential Remarker for a Minimal, Synthetic Genome, Bronze Medal;
Freiburg Software 2009 (Germany) SynBioWave – A Collaborative Synthetic Biology Software Suite, Silver Medal;
Minnesota 2009 (United States) Computational synthetic biology: How the Synthetic Biology Software Suite can guide wet-lab experiments, Gold Medal;
USTC Software 2009 (United States) Automatic Biological Circuit Design, Gold Medal;
Washington-Software 2009 (United States) LegoRoboBricks for Automated BioBrick Assembly, Silver Medal.
2010
Best Software Tool Winner (2010)
USTC_Software 2010 (China) developed “iGaME” an experimental video game which aims at instructing non-biologists to design and improve biological systems. Winner Best Software Tool, Gold Medal.
Teams in the Software Tools track (2010)
Freiburg Software 2010 (Germany) SynBioWave 2.0 - A Collaborative Toolkit for Synthetic Biology, Silver Medal;
METU_Turkey_Software 2010 (Turkey) BIO-GUIDE, Silver Medal;
UIUC-Illinois-Software 2010 (United States) BioMORTAR, Silver Medal;
VT-ENSIMAG_Biosecurity 2010 (United States) Design and development of the GenoTHREAT gene sequence screening software, Bronze Medal, Safety Commendation;
ZJU-China 2010 (China) Bach: gene composer, Gold Medal.
2011
Best Software Tool Winners (2011)
BU_Wellesley_Software 2011 (United States) created a collection of software tools that address specific technical synthetic biology challenges, including "G-Nome Surfer Pro" for research, "Trumpet" and "Optimus Primer" for design, and "Puppetshow" and "eLabNotebook" for the construction of those designs. Gold Medal, Advance to Championship, Winner Best Software Tool.
Teams in the Software Tools track (2011)
CBNU-Korea 2011 (Republic of Korea) GOD, Genome Organization & Design for synthetic minimal genome;
ENSPS-Strasbourg 2011 (France) Biobricks model generator for electronic simulators, Advance to Championship, Bronze Medal;
HUST-China 2011 (China) Super E.coli Architect;
METU-BIN Ankara 2011 (Turkey) M4B: Mining for Biobricks, Bronze Medal;
NYC_Software 2011 (United States) Deinococcus Genome Sequencing & Registry/ Biobrick Tools;
USTC-Software 2011 (China) Lachesis, Advance to Championship, Bronze Medal.
2012
Best Software Winners (2012)
Johns_Hopkins-Software 2012 (United States) developed “AutoGene” - an innovative CAD tool used to automate the design process of synthetic DNA sequences. Advance to Software Jamboree, Gold Medal, Winner Best Software, Best SBOL Based Tool.
USTC-Software 2012 (China) built a suite of applications using reverse engineering techniques to get mathematical models, such as ordinary differential equations, directly from the experimental data, thereby providing researchers with efficient workflows for building feasible biological designs. Advance to Software Jamboree, Gold Medal, Winner Best Software.
Wellesley_HCL 2012 (United States) developed “Synbio Search” - an online tool that generates data sheets for biological parts by aggregating data from various publicly available resources, “MoClo Planner” - a tool that visualizes the Golden Gate Modular Cloning process and facilitates hierarchical design and production of multi-gene constructs, and “SynFlo” - an interactive installation to illustrate core concepts of synthetic biology in outreach programs. Advance to Software Jamboree, Gold Medal, Winner Best Requirements Engineering, Best Eugene Based Design, Best SBOL Based Tool.
Teams in the Software track (2012)
CBNU-Korea 2012 (Republic of Korea) BUGS: Brick and Unique minimal Genome Software, Advance to Software Jamboree, Silver Medal;
SUSTC-Shenzhen-A 2012 (China) BioSearch-An iPhone App for Parts registry, Advance to Software Jamboree, Silver Medal;
SUSTC-Shenzhen-B 2012 (China) Theoretical modeling and experimental measurement of transcription terminator efficiency, Advance to Software Jamboree, Gold Medal;
SYSU-Software 2012 (China) BiArkit, A Versatile Toolkit For Synthetic Biology, Advance to Software Jamboree, Gold Medal;
UT-Tokyo-Software 2012 (Japan) Software tools for iGEMers: BioBrick/Project Search & Tutorials, Advance to Software Jamboree, Gold Medal;
UTP-Software 2012 (Panama) Bricks, Mutagenesis and Energy Software Tools, Advance to Software Jamboree, Silver Medal.
2013
Software Track Winner (2013)
SYSU-Software 2013 (China) designed CAST (Computer Aided Synbio Tool) that can automatically perform the regulatory networks and gene circuits designing, modeling, vector designing, and proposal building, Winner Best Software Project, Gold Medal.
Teams in the Software Tools track (2013)
AMU-Poznan 2013 (Poland) sh-miR designer - tool for construction of RNA interference reagents: sh-miRs, Silver Medal;
Shenzhen_BGIC_0101 2013 (China) Genovo - a Computer-Aided Design (CAD) tool used for de novo design of genome, Gold Medal;
SUSTC-Shenzhen-B 2013 (China) Circuit+, Gold Medal;
UESTC 2013 (China) Nebula - a biological circuit design tool, Gold Medal;
USTC-Software 2013 (China) Gene Network Analyze and Predict (gNAP), Gold Medal;
Wellesley_Desyne 2013 (United States) Enhancing Bio-Design with Next-Generation Human-Computer Interaction, Gold Medal;
XMU_Software 2013 (China) BioBrick evaluation and optimization software suit and lab assistant tool, Gold Medal.
2014
Best Supporting Software Award introduced for teams not in the Software Track
Software Track Winner (2014)
SYSU-Software 2014 (China) developed FLAME - Framework-based Layout And Metacircuit design Engine - a software tool that combines a simplified design procedure, a new and effective simulation module, and wetlab validation to make complex biological circuits more accessible to synthetic biologists. Winner Best Software Project, Gold Medal.
Teams in the Software track: AMU-Poznan 2014 (Poland) sh-miR designer v2.0 - a user-friendly tool for sh-miR prediction, Gold Medal; HFUT_CHINA 2014 (China) BioFunctional Designer, Gold Medal; Michigan_Software 2014 (United States) ProtoCat: Increasing Reproducibility Through Protocol Sharing And Review, Bronze Medal; PoznanSoft 2014 (Poland) MUFASA: Multiple fragments assembler for scarless cloning of big genetic constructs, Bronze Medal; SJTU-Software 2014 (China) Evaluation, Visualization, Simplification, Standardization of BioBrick Information and Biosystem Design, Gold Medal; UCSD_Software 2014 (United States) SBiDer: Synthetic Biocircuit Developer, Gold Medal; UESTC-Software 2014 (China) CRISPR-X: a sgRNA design tool for genome editing in synthetic biology, Gold Medal; USTC-Software 2014 (China) BioPano-A platform which helps you figure out relationships between various substances in the bacteria, Gold Medal; Vanderbilt_Software 2014 (United States) Darwin: A Version Control System for Synthetic Biology, Bronze Medal.
Best Supporting Software Winners (2014)
Heidelberg 2014 (Germany) developed “iGEM@home” - a platform that deals with the common problem of insufficient computing resources for iGEM teams, “Linker Software” that predicts the perfect linker based on protein folding structure, and “MidnightDoc” - an easy-to-use platform for lab documentation. Winner Best Supporting Software, Grand Prize Winner, iGEMer’s Prize, Gold Medal, Undergrad Division.
Aachen 2014 (Germany) developed “Measurearty” that automatically detects pathogens from chip photos, “Serial Client” - a Windows Desktop app that plots data coming in on a serial (USB) port live and saves it for later export to Excel, and “Timeseries Labeller” that automatically recognize timestamps from filenames. Winner Best Supporting Software, Best Measurement Project, Safety Commendation, Gold Medal, Overgrad Division.
2015
Software Track Winners (2015)
SYSU-Software 2015 (China) developed CORE – Crowdsourcing Open Redesign Engine – an open and extensible software that allows users to design, share and cooperate in synthetic biology. Winner Best Software Project, Gold Medal.
UESTC_Software 2015 (China) developed MCCAP – Minimal Cell Construct and Analyse Panel – a software targeted for screening the essential genes that could aid in identifying antimicrobial drug targets, creating the chassis of an artificial cell, promoting the synthesis of engineered bacterial strains, and determine the last universal common ancestor. Nominated for Best Software Project, Gold Medal.
Teams in the Software track (2015): HFUT-China 2015 (China) BioDesigner, Gold Medal; Korea_U_Seoul 2015 (Republic of Korea) The pathfinder for Synthetic Biologists, Gold Medal; Michigan_Software 2015 (United States) ProtoCat: Increasing Reproducibility Through Protocol Sharing And Review, Bronze Medal; SJTU-Software 2015 (China) BASE: a multi-level biobrick evaluation and visualization system, Gold Medal; Toronto 2015 (Canada) A Genetically Engineered Solution for Oil Sand Tailings: Enhanced Bioremediation by Toluene Degrading Bacteria, Silver Medal; USTC-Software 2015 (China) BioBLESS-Biological Boolean Logic Evaluation & Systematization based on Simulation, Gold Medal.
Best Software Tool Special prize (2015)
Czech Republic 2015 (Czech Republic) engineered the Input Output Diploid (IOD) bands. Winner Best Software Tool, Best Model, Best Health and Medicine Project, First Runner Up, Gold Medal, Undergrad Division.
Waterloo 2015 (Canada) Re-engineered CRISPR-Cas9 with functional applications in eukaryotic systems. Winner Best Software Tool, Gold Medal, Overgrad Division.
Cambridge-JIC 2015 (United Kingdom) developed “Microscopy Server” that enables users to turn their Raspberry Pi into a web-accessible microscope. Nominated for Best Software Tool, Gold Medal, Undergrad Division.
Heidelberg 2015 (Germany) developed software for Making Aptamers Without Selex (MAWS) and for Joining Aptamers Without Selex (JAWS). Nominated for Best Software Tool, Winner iGEMers Prize, Best Foundational Advance Project, Second Runner Up, Undergrad Division.
Aachen 2015 (Germany) developed a suite of calibration and control software "Master Control Program" to test and run DIY bioreactors. Nominated for Best Software Tool, Winner Best Manufacturing Project, Gold Medal, Overgrad Division.
2016
Software Track Winners (2016)
Michigan Software 2016 (United States) created ProtoCat, a database that integrates a crowd-sourced ratings and comments system to serve as a protocol curator that enables wet lab investigators to compare various protocol efficacies, quantify a protocol’s acceptance within the scientific community, and provide an avenue through which experiential knowledge can be communicated. Winner Best Software Project, Gold Medal.
Teams in the Software track (2016): HFUT-China 2016 (China) BioDesigner Coral, Silver Medal; SJTU-Software 2016 (China) iMAP—iGEMers' Management and Alliance Platform, Gold Medal; SYSU-Software 2016 (China) CRAFT – Community-based Retro-synthetic Analysis Functional platform, Gold Medal; UESTC-software 2016 (China) Bio101: DNA Information Storage System, Gold Medal; USTC-Software 2016 (China) BioHub, Gold Medal.
Best Software Tool Special Prize (2016)
Valencia UPV 2016 (Spain) developed HYPE-IT software that gathers and integrates a forum, a blog, a news feed, a complete targets database, our scoring system, a gene viewer, and a hierarchy of groups. Wnner Best Software Tool, Best Hardware, Gold Medal, Undergrad Division.
LMU-TUM Munich 2016 (Germany) adapted software to convert an Ultimaker 3D printer into a bioprinter. Winner Best Software Tool, Best Hardware, Best Manufacturing Project, Grand Prize Winner, Gold Medal, Overgrad Division.
Warwick 2016 (United Kingdom) created “Tunable gRNA Designer” - a software tool that uses a DNA sequence input, and designs a list of gRNA sequences as output. Nominated for Best Software Tool, Gold Medal, Undergrad Division.
BostonU_HW 2016 (United States) developed Neptune, an open-source software tool for designing a microfluidic chip. Nominated for Best Software Tool, Gold Medal, Undergrad Division.
EPFL 2016 (Switzerland) modified Cello and Database. Nominated for Best Software Tool, Gold Medal, Overgrad Division
Groningen 2016 (Netherlands) developed software for CryptoGErM, which encrypts a message and translates it to DNA. Nominated for Best Software Tool, Winner Best Information Processing Project, Gold Medal, Overgrad Division.
INSA-Lyon 2016 (France) created a software tool that predicts the structure of aptamers by converting the aptamer to RNA, then computing its structure, re-convert to DNA and minimize the free energy to adjust atom coordinates. Nominated for Best Software Tool, Winner Best Diagnostics Project, Gold Medal, Undergrad Division.
2017
Software Track Winner (2017)
SYSU-Software 2017 (China) developed S-DIN—Search engine and Design platform for Inspiration with Network analysis. Winner Best Software Project, Gold Medal.
Teams in the Software track (2017): Florida_Atlantic 2017 (United States) Welcome to the Machine: Developing a Novel Biosensor for Artemisinin, Bronze Medal; HFUT-China 2017 (China) BioDesigner Dolphin, Gold Medal; IIT-Madras 2017 (India) A digital information catalogue of host organisms for synthetic biology, with supportive software tools, Silver Medal; Michigan_Software 2017 (United States) ProtoCat - Collaborating Towards Success, Gold Medal; NCTU_Formosa 2017 (Taiwan) Parabase – A Simple and Applicable Peptide Prediction System with Validation of Artificial Intelligence, Gold Medal; SJTU-Software 2017 (China) BAT: BiobrickAssist Technology, a search & evaluation engine for biobricks, Bronze Medal; USTC-Software 2017 (China) Biohub 2.0, Gold Medal.
Best Software Tool Special Prize (2017)
Heidelberg 2017 (Germany) developed AIGEM – Artificial Intelligence for Genetic Evolution Mimiking. Winner Best Software Tool, Best Foundational Advance Project, Best Integrated Human Practices, Finalist, Gold Medal, Undergrad Division.
Munich 2017 (Germany) developed CascAID, a potentially universal tool for nucleic acid detection. Winner Best Software Tool, Best Hardware, Best Diagnostics Project, Best Model, Best Applied Design, Finalist, Gold Medal, Overgrad Division.
CLSB-UK 2017 (United Kingdom) created several software tools, including Synthetic Biology Bot, Toehold Switch Tools, and Fluorometer and Densitometer Interpreter. Winner Best Software Tool, Best Hardware, Best New Composite Part, Best Integrated Human Practices, Gold Medal, High School Division.
Fudan 2017 (China) created “Netro” to analyze gene transcription networks and “Netro Fudan” to aid in understanding their model and gaining insights into biochemical reactions in cells. Nominated for Best Software Tool, Winner Best Therapeutics Project, Gold Medal, Undergrad Division.
EPFL 2017 (Switzerland) created “Toehold Designer” for generating new toehold switches in-silico. Nominated for Best Software Tool, Winner Best Education & Public Engagement, Gold Medal, Undergrad Division.
Valencia UPV 2017 (Spain) developed PlantLabCo, an open source software tool for plant synthetic biology. Nominated for Best Software Tool, Gold Medal, Undergrad Division.
Lethbridge 2017 (Canada) developed biosecurity software to aid in detecting DNA containing funtional toxin sequences. Nominated for Best Software Tool, Gold Medal, Overgrad Division.
Bielefeld-CeBiTec 2017 (Germany) created a software suite for analysis of Oxford Nanopore sequencing data of DNA containing unnatural bases, and a customized database for analysis of mutations at a specific position. Nominated for Best Software Tool, Winner Best Foundational Advance Project, Best New Basic Part, Gold Medal, Overgrad Division.
2018
Software Track (2018)
UESTC-Software 2018 (China) developed BioMaster, an integrated bio-brick database with the function of promoter prediction. Winner Best Software Project, Gold Medal.
Teams in the Software track: SJTU-software 2018 (China) Metlab: a metabolic network alignment tool, Silver Medal; SYSU-Software 2018 (China) CO-RAD:Collaborative optimization platform with recommendation, analysis and design, Silver Medal; Tongji-Software 2018 (China) Alpha Ant, Gold Medal; USTC-Software 2018 (China) Biohub 3.0, Silver Medal.
Best Software Special Prize (2018)
Valencia_UPV 2018 (Spain) developed Printeria Controller, an intuitive software that provides a user-friendly interface to access the capabilities of Printeria. Winner Best Software, Best Hardware, Best New Application Project, Best Model, Grand Prize, Gold Medal, Undergrad Division.
Munich 2018 (Germany) developed Sequ-into, which detects contaminations in third generation sequencing data in a highly sensitive manner. Winner Best Software, Best Manufacturing Project, Best Entrepreneurship, Finalist, Bronze Medal, Overgrad Division.
Nominees for Best Software Special Prize: BostonU_HW 2018 (United States) Gold Medal; Calgary 2018 (Canada) Gold Medal; EPFL 2018 (Switzerland) Gold Medal; HebrewU 2018 (Israel) Gold Medal, Winner Best Plant Synthetic Biology, Overgrad Division; IISc-Bangalore 2018 (India) Gold Medal; Paris Bettencourt 2018 (France) Gold Medal; TecCEM 2018 (Mexico) Gold Medal; UNSW Australia 2018 (Australia) Gold Medal; Virginia 2018 (United States) Bronze Medal.
2019
Software Track (2019)
UESTC-Software 2019 (China) BioMaster 2.0, integrated and user-friendly database for synthetic biology. Winner Best Software Project, Nominated for Best Hardware, Gold Medal.
USTC-Software 2019 (China) developed Foresyn, a user-friendly platform that allows users to build their models for flux analysis, get visualized output, and easily share with others. Nominated for Best Software Project, Gold Medal.
Teams in the Software track: Potsdam 2019 (Germany) TherMaL.UP - Evolution of thermophilic proteins with a neural network-based approach, Silver Medal; SJTU-software 2019 (China) Phosyme: an online database with toolbox focusing on the plant synthetic biology, Gold Medal; Tongji_Software 2019 (China) Pathlab: An integrated platform for pathway construction with enzyme information, Gold Medal.
Best Software Tool Special Prize (2019)
Calgary 2019 (Canada) built 2 software tools: BOTS to optimize BioBricks for synthesis, and iGAM to help develop genetic algorithms. Winner Best Software Tool, Gold Medal, Undergrad Division.
DTU-Denmark 2019 (Denmark) developed LAEP, a new state-of the art of software that can generate promoter sequences for different organisms. Winner Best Software Tool, Gold Medal, Overgrad Division.
Nominees for Best Software Tool: Grenoble-Alpes 2019 (France) NeuroDrop software, Gold Medal; SASTRA_Thanjavur 2019 (India) Predictive modelling of the efficacy of toehold switches, Silver Medal; SMMU-China 2019 (China) An original analysis system, Silver Medal; SUSTech_Shenzhen 2019 (China) Alive Cell Tracking Alpha, Gold Medal; Sydney_Australia 2019 (Australia) Codonator 3000, Gold Medal.
2020
Software Track (2020)
Concordia-Montreal 2020 (Canada) developed “ASTROBIO” - an open-source, differential gene expression analysis software and database for microgravity researchers. Winner Best Software Project, Gold Medal.
Imperial_College 2020 (United Kingdom) developed “SOAP Lab - an open-source web UI that infers genetic circuit designs from SBOL data files and customizes an assembly plan based on the user’s specifications. Nominated for Best Software Project, Gold Medal.
UESTC-Software 2020 (China) developed “CPD3DS”- Classification of Protein Domains in 3D Shape - a user-friendly website for retrieval, analyses and visualization of classified protein domains. Nominated for Best Software Project, Gold Medal.
Teams in the Software track: Linkoping 2020 (Sweden) ClusteRsy: A user-friendly software for transcriptomic analysis and biomarker discovery. Gold Medal; SJTU-software 2020 (China) RICAID. Gold Medal; SYSU-Software 2020 (China) Maloadis - Machine Learning based Optimization and automated Design Platform with Image Search. Gold Medal; Tongji_Software 2020 (China) Synthesis Navigator. Gold Medal; UC_Davis 2020 (United States) Expanding the gene regulatory toolkit in filamentous fungi through bioinformatics-directed genome mining. Gold Medal; UIUC_Illinois 2020 (United States) Viralizer – Modeling Covid-19 mutations and binding energies to design potential antibodies. Silver Medal; USTC-Software 2020 (China) Protein molecular simulation toolchain.
Best Software Tool Special Prize (2020)
BITSPilani-Goa_India 2020 (India) built iGEM WikiSync, an integration tool that allows CI/CD software to upload files to iGEM servers. Winner Best Software Tool, Gold Medal, Undergrad Division.
TAU_Israel 2020 (Israel) developed Staubility Enhancer for designing embeddings of target genes into host genomes, and Staubility EFM Optimizer for designing multiple genetic sequences in tandem. Winner Best Software Tool, Gold Medal, Overgrad Division.
TAS_Taipei 2020 (Taiwan) developed VisulapH, software used to provide an inexpensive, fast, accurate, and precise result for pH measurement. Winner Best Software Tool, Best Measurement, Best New Basic Part, Best New Composite Part, Best Part Collection, Gold Medal, High School Division.
Nominees for Best Software Tool: DTU-Denmark 2020 (Denmark) Morphologizer and Mycemulator. Gold Medal; Grenoble_Alpes 2020 (France) HermAs communication protocol and Pythie web interface. Gold Medal; GunnVistaPingry_US 2020 (United States) Odigos Guide Predictor, Model Generator, and Model Compare. Gold Medal; Rochester 2020 (United States) Endometriosis Risk Calculator and Biomarker Database. Gold Medal; UiOslo_Norway 2020 (Norway) Sal.Coli. Gold Medal; Vilnius-Lithuania 2020 (Lithuania) “Onflow” to predict various parameters of Lateral flow assay tests. Gold Medal, Grand Prize Winner, Undergrad Division.
2021
Software Track (2021)
Tongji_Software 2021 (China) built “Phage-MAP” – computational methods (alignment-based and alignment-free) of identifying phage-host interactions. Winner Best Software Project, Gold Medal.
SJTU-Software 2021 (China) built a deep learning model to assist in probe design for Nano DNA machines. Nominated for Best Software Project, Gold Medal.
Teams in the Software track: Phystech_Moscow 2021 (Russian Federation) Tool for miRNA-lncRNA interaction prediction. Gold Medal; SYSU-Software 2021 (China) Phoebus. Silver Medal; USTC-Software 2021 (China) CAT : Convenient and Accurate Tool. Silver Medal.
Best Software Tool Special Prize (2021)
ZJU-China 2021 (China) developed “Expmeasure” to provide a GUI interface based on R shiny, which enables all iGEMers to perform advanced statistical methods. Winner Best Software Tool, Gold Medal, Undergrad Division.
Marburg 2021 (Germany) created a comprehensive chloroplast database that can provide deep insights into the development and for engineering plants. Winner Best Software Tool, Gold Medal, Grand Prize Winner, Overgrad Division.
Nominees for Best Software Tool: Aachen 2021 (Germany) Storagene. Gold Medal; CSMU_Taiwan 2021 (Taiwan) Circular DNA Sequence Design. Gold Medal; CSU_CHINA 2021 (China) Interactive CA Based Gene Circuit visual analytics system. Gold Medal; Heidelberg 2021 (Germany) Graph Neural Network. Gold Medal; Kyoto 2021 (Japan) DLAEMON (diseased leaves assessment by efficient machine learning on neural network) and NOBITA (numericalization of brightness of image for one touch assessment). Gold Medal; Tec-Monterrey 2021 (Mexico) Primer design by PrimedRPA, Toehold Design with Toehold Switch Creator, and Thermodynamic Analysis with ViennaRNA. Gold Medal; TU_Darmstadt 2021 (Germany) GoGEM. Gold Medal; Vilnius-Lithuania 2021 (Lithuania) entropy fragment based approach able to generate an aptamer sequence and bioinformatics tools. Gold Medal.
2022
iGEM introduces the Software & AI Village
Software & AI Track (2022)
William_and_Mary 2022 (United States) built “ChassEASE” which predicts the optimal chassis for a specific environment, or the most favorable environment for a predetermined chassis, leading to safer, more effective, fieldable, and robust genetic circuits. Winner Best Software & AI Project, Gold Medal.
Teams in the Software & AI Village: PUMC_CHINA 2022 (China) Single-cell lineage inference tool based on lineage clustering. Bronze Medal; SJTU-software 2022 (China) Deep Learning-based Enzyme-Constrained Genome-scale Metabolic model (DL-ecGEM) for actinomycetes. Gold Medal; SYSU-Software 2022 (China) “LOUPE” for the discovery of the currently unknown defense genes in prokaryotes. Gold Medal; Tongji_Software 2022 (China) AcrGPS: Anti-CRISPR Genome-based Predicting Software. Bronze Medal; USTC-Software 2022 (China) MEI: Modified Enzyme Interface. Silver Medal.
Best Software Tool Special Prize (2022)
Munich 2022 (Germany) developed “OSCAR” - Open Source Chimeric Antigen Receptors - a database for cataloging and sharing chimeric antigen receptors. Winner Best Software Tool, TOP 10, Gold Medal, Undergrad Division.
WWU_Muenster 2022 (Germany) developed a user-friendly command line tool that comprises Flux Scanning based on Enforced Objective fFux (FSEOF) for any metabolite of interest in a genome-scale metabolic models. Winner Best Software Tool, TOP 10, Gold Medal, Overgrad Division.
Nominees for Best Software Tool (2022)
CAU_China 2022 (China) software tool to predict nutrient concentrations in a solid matrix based on Poisson's equations and Monod's equations. TOP 10, Best Biomanufacturing Project, Gold Medal;
Chalmers-Gothenburg 2022 (Sweden) PLOP - Polymer Length Optimization Program. Gold Medal;
Fudan 2022 (China) PartHub, a software tool that contains information on almost all of the Registry of Standard Biological Parts from 2004 onwards. Best Measurement, Best New Basic, Best Part Collection, Gold Medal;
IISER_Mohali 2022 (India) KAMI: Kwick Aptamer-based Motif Identification. Gold Medal;
INSA_Lyon1 2022 (France) FIAT LUX app for analyzing images of plant infections by luminescent bacteria. TOP 10, Best Food & Nutrition Project, Best Hardware, Best New Composite Part, Gold Medal, First Runner Up, Undergrad Division;
MIT_MAHE 2022 (India) GRASP - Generating Random Alanine Scanned Peptides. Gold Medal;
Sogang_Korea 2022 (Republic of Korea) SynBioBot software. Gold Medal;
TAU_Israel 2022 (Israel) user-friendly website with a software tool for the automatic generation of switch modules in the 5’-UTR of an mRNA for cell-specific translation. Best Model, Gold Medal, Overgrad Division;
Tsinghua 2022 (China) “kmer2vec” a sequence comparison software and “Promoter_Transformer” a promoter strength prediction software. Silver Medal.
We are proud of these and other iGEM teams that have created a valuable legacy in software development for synthetic biology. You can check out the source code of their software on the dedicated repository on iGEM's GitLab. Please join us in congratulating these teams, and in celebrating the innovations in software that the 2023 teams will bring to the Grand Jamboree!
