10 years of SBOL Visual - Initial Commit

content/sbolv-10-years/acs-2012.md

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+---  
+title: 2012 ACS Synthetic Biology Issues  
+
+# View.  
+#   1 = List  
+#   2 = Compact  
+#   3 = Card  
+#   4 = Citation  
+view: 3  
+
+# Optional header image (relative to `static/img/` folder).  
+header:  
+  caption: ""  
+  image: ""  
+---
+# Summary
+
+- **Total Articles Analyzed:** 63  
+- **Total Figures in All Articles:** 340  
+- **Figures Compatible with SBOL Visual:** 87 (25.59%)  
+- **Figures Compatible with SBOL Visual & Fully Compliant:** 36 (41.38%)  
+- **Figures Compatible with SBOL Visual & Following Best Practices:** 18 (20.69%)
+# Individual issues
+
+## January
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Engineering Artificial Small RNAs for Conditional Gene Silencing in Escherichia coli|1|0||
+|j5 DNA Assembly Design Automation Software|3|1||
+
+## April
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|SYNZIP Protein Interaction Toolbox: in Vitro and in Vivo Specifications of Heterospecific Coiled-Coil Interaction Domains|1|0||
+
+## July
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|ePathBrick: A Synthetic Biology Platform for Engineering Metabolic Pathways in E. coli|4|0||
+
+## August
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|An End-to-End Workflow for Engineering of Biological Networks from High-Level Specifications|4|2||
+|Computational Modeling of Synthetic Microbial Biofilms|1|1|:star:|
+|Hierarchical Modeling for Synthetic Biology|7|7|:star:|
+|Specification and Simulation of Synthetic Multicelled Behaviors|3|3|:star:|
+
+## September
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|A Synthetic Biology Approach to Understanding Cellular Information Processing|2|0||
+
+## October
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Stable Maintenance of Multiple Plasmids in E. coli Using a Single Selective Marker|2|0||
+
+## November
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Rational Design of Escherichia coli for l-Isoleucine Production|1|1|:star:|
+|Genetic Circuit Performance under Conditions Relevant for Industrial Bioreactors|1|1|:star:|

content/sbolv-10-years/acs-2013.md

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+---  
+title: 2013 ACS Synthetic Biology Issues  
+
+# View.  
+#   1 = List  
+#   2 = Compact  
+#   3 = Card  
+#   4 = Citation  
+view: 3  
+
+# Optional header image (relative to `static/img/` folder).  
+header:  
+  caption: ""  
+  image: ""  
+---
+# Summary
+
+- **Total Articles Analyzed:** 80  
+- **Total Figures in All Articles:** 408  
+- **Figures Compatible with SBOL Visual:** 99 (24.26%)  
+- **Figures Compatible with SBOL Visual & Fully Compliant:** 61 (61.62%)  
+- **Figures Compatible with SBOL Visual & Following Best Practices:** 36 (36.36%)
+# Individual issues
+
+## February
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Synthesizing Biomolecule-Based Boolean Logic Gates|3|3|:star:|
+|Self-Assembly of Synthetic Metabolons through Synthetic Protein Scaffolds: One-Step Purification, Co-immobilization, and Substrate Channeling|2|2|:star:|
+
+## March
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Tuning Primary Metabolism for Heterologous Pathway Productivity|1|0||
+
+## May
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Dynamic Modeling of Cellular Populations within iBioSim|1|0||
+|AutoBioCAD: Full Biodesign Automation of Genetic Circuits|2|2|:star:|
+|Reverse Engineering Validation using a Benchmark Synthetic Gene Circuit in Human Cells|1|1|:star:|
+|SBROME: A Scalable Optimization and Module Matching Framework for Automated Biosystems Design|2|2|:star:|
+
+## June
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Pigeon: A Design Visualizer for Synthetic Biology|1|1|:star:|
+
+## July
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Synthetic Biology of Antimicrobial Discovery|1|1|:star:|
+
+## August
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Synthetic Gene Circuit-Mediated Monitoring of Endogenous Metabolites: Identification of GAL11 as a Novel Multicopy Enhancer of S-Adenosylmethionine Level in Yeast|3|3|:star:|
+|Retroactivity Controls the Temporal Dynamics of Gene Transcription|1|0||
+|Analysis and Design of a Genetic Circuit for Dynamic Metabolic Engineering|1|0||
+
+## September
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Randomized BioBrick Assembly: A Novel DNA Assembly Method for Randomizing and Optimizing Genetic Circuits and Metabolic Pathways|5|5|:star:|
+|Visualization of Evolutionary Stability Dynamics and Competitive Fitness of Escherichia coli Engineered with Randomized Multigene Circuits|2|2|:star:|
+
+## October
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Tuning Response Curves for Synthetic Biology|3|0||
+|Engineering the esaR Promoter for Tunable Quorum Sensing-Dependent Gene Expression|1|0||
+|Reliable Prediction of Complex Phenotypes from a Modular Design in Free Energy Space: An Extensive Exploration of the lac Operon|1|0||
+|Expanding the Boolean Logic of the Prokaryotic Transcription Factor XylR by Functionalization of Permissive Sites with a Protease-Target Sequence|6|0||
+|Genetic Sensor for Strong Methylating Compounds|2|2|:star:|
+
+## November
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Discovery of Cryptic Polyketide Metabolites from Dermatophytes Using Heterologous Expression in Aspergillus nidulans|2|2|:star:|
+|Sequence, Cloning, and Analysis of the Fluvirucin B1 Polyketide Synthase from Actinomadura vulgaris|1|1|:star:|
+|Multiplex Iterative Plasmid Engineering for Combinatorial Optimization of Metabolic Pathways and Diversification of Protein Coding Sequences|4|3||
+|Refactoring the Silent Spectinabilin Gene Cluster Using a Plug-and-Play Scaffold|2|2|:star:|
+|Facile Method for Site-specific Gene Integration in Lysobacter enzymogenes for Yield Improvement of the Anti-MRSA Antibiotics WAP-8294A and the Antifungal Antibiotic HSAF|2|2|:star:|
+
+## December
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Artificial Conversion of the Mating-Type of Saccharomyces cerevisiae without Autopolyploidization|4|0||
+|Cell Polarity-Driven Instability Generates Self-Organized, Fractal Patterning of Cell Layers|1|0||
+|Yeast Oligo-Mediated Genome Engineering (YOGE)|1|0||

content/sbolv-10-years/acs-2014.md

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+---  
+title: 2014 ACS Synthetic Biology Issues  
+
+# View.  
+#   1 = List  
+#   2 = Compact  
+#   3 = Card  
+#   4 = Citation  
+view: 3  
+
+# Optional header image (relative to `static/img/` folder).  
+header:  
+  caption: ""  
+  image: ""  
+---
+# Summary
+
+- **Total Articles Analyzed:** 118  
+- **Total Figures in All Articles:** 531  
+- **Figures Compatible with SBOL Visual:** 113 (21.28%)  
+- **Figures Compatible with SBOL Visual & Fully Compliant:** 53 (46.9%)  
+- **Figures Compatible with SBOL Visual & Following Best Practices:** 27 (23.89%)
+# Individual issues
+
+## January
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Taking Control over Control: Use of Product Sensing in Single Cells to Remove Flux Control at Key Enzymes in Biosynthesis Pathways|1|1|:star:|
+
+## February
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Bi-HAC Vector System toward Gene and Cell Therapy|3|0||
+|Engineered DNA Sequence Syntax Inspector|2|2|:star:|
+
+## March
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Using Synthetic Biological Parts and Microbioreactors to Explore the Protein Expression Characteristics of Escherichia coli|1|1|:star:|
+|Improving the Gene-Regulation Ability of Small RNAs by Scaffold Engineering in Escherichia coli|2|2|:star:|
+|Toward a Generalized and High-throughput Enzyme Screening System Based on Artificial Genetic Circuits|2|0||
+
+## April
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Engineering Multicellular Logic in Bacteria with Metabolic Wires|2|2|:star:|
+|Evolved Quorum Sensing Regulator, LsrR, for Altered Switching Functions|1|0||
+|Generic Metric to Quantify Quorum Sensing Activation Dynamics|2|1||
+|Reprogramming Microbes to Be Pathogen-Seeking Killers|1|1|:star:|
+|Quorum Sensing-Modulated AND-Gate Promoters Control Gene Expression in Response to a Combination of Endogenous and Exogenous Signals|1|0||
+
+## May
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Optimization of a Yeast RNA Interference System for Controlling Gene Expression and Enabling Rapid Metabolic Engineering|1|1|:star:|
+|MicroRNA-Based Single-Gene Circuits Buffer Protein Synthesis Rates against Perturbations|2|0||
+
+## June
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Gene Position More Strongly Influences Cell-Free Protein Expression from Operons than T7 Transcriptional Promoter Strength|2|2|:star:|
+
+## August
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|PR-PR: Cross-Platform Laboratory Automation System|2|2|:star:|
+|Optimal Part and Module Selection for Synthetic Gene Circuit Design Automation|2|1||
+|Biological 2-Input Decoder Circuit in Human Cells|1|0||
+
+## September
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|General Applicability of Synthetic Gene-Overexpression for Cell-Type Ratio Control via Reprogramming|1|0||
+|Framework for Engineering Finite State Machines in Gene Regulatory Networks|3|1||
+
+## October
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Development of an Artificial Calcium-Dependent Transcription Factor To Detect Sustained Intracellular Calcium Elevation|1|0||
+|Rule-Based Design of Synthetic Transcription Factors in Eukaryotes|1|0||
+
+## November
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Near-infrared Light Responsive Synthetic c-di-GMP Module for Optogenetic Applications|3|3|:star:|
+|Refactoring and Optimization of Light-Switchable Escherichia coli Two-Component Systems|2|1||
+|A Golden Gate Modular Cloning Toolbox for Plants|2|1||
+
+## December
+
+|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
+| :---: | :---: | :---: | :---: |
+|Systematic Transfer of Prokaryotic Sensors and Circuits to Mammalian Cells|3|3|:star:|
+|Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation|1|0||
+|Natural LacI from E. coli Yields Faster Response and Higher Level of Expression than the LVA-Tagged LacI|1|1|:star:|
+|Standardization of Functional Reporter and Antibiotic Resistance Cassettes to Facilitate the Genetic Engineering of Filamentous Fungi|1|1|:star:|
+|Solving a Four-Destination Traveling Salesman Problem Using Escherichia coli Cells As Biocomputers|2|0||