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PrashantVaidyanathan merged 3 commits into from
Feb 4, 2025
Merged

Fix SBOL V - 10 years typo #256

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632b871
Fixed link issues.
PrashantVaidyanathan Feb 1, 2025
5888fc2
Merge branch 'master' of https://github.com/SynBioDex/SbolStandardWeb…
PrashantVaidyanathan Feb 4, 2025
5a5c0e5
Fix compliant spelling error
PrashantVaidyanathan Feb 4, 2025
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4 changes: 2 additions & 2 deletions content/sbolv-10-years/_index.md
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Expand Up @@ -28,8 +28,8 @@ For each manuscript, we:
- **Reviewed the Main Manuscript:** Focused on the published figures.
- **Counted the Figures:** Recorded the total number of images per paper.
- **Assessed SBOL Visual Compatibility:** Identified which figures could be considered as SBOL Visual images.
- **Checked Compliance:** Determined whether SBOL Visual complaint figures followed the SBOL Visual standard
- **Checked Best Practices:** Determined whether SBOL Visual complaint figures followed recommended SBOL Visual best practices.
- **Checked Compliance:** Determined whether SBOL Visual compliant figures followed the SBOL Visual standard
- **Checked Best Practices:** Determined whether SBOL Visual compliant figures followed recommended SBOL Visual best practices.

We have also listed the [guidelines we followed while evaluating the figures.](guidelines)

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14 changes: 7 additions & 7 deletions content/sbolv-10-years/acs-2012/index.md
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Expand Up @@ -25,26 +25,26 @@ header:

## January

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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:|
Expand All @@ -53,19 +53,19 @@ header:

## September

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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:|
20 changes: 10 additions & 10 deletions content/sbolv-10-years/acs-2013/index.md
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Expand Up @@ -25,20 +25,20 @@ header:

## February

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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:|
Expand All @@ -47,34 +47,34 @@ header:

## June

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
Expand All @@ -84,7 +84,7 @@ header:

## November

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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:|
Expand All @@ -94,7 +94,7 @@ header:

## December

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
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22 changes: 11 additions & 11 deletions content/sbolv-10-years/acs-2014/index.md
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Expand Up @@ -25,28 +25,28 @@ header:

## January

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
Expand All @@ -56,50 +56,50 @@ header:

## May

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
|Article|No. of SBOL Visual compliant 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||
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24 changes: 12 additions & 12 deletions content/sbolv-10-years/acs-2015/index.md
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Expand Up @@ -25,15 +25,15 @@ header:

## January

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Model-Driven Engineering of Gene Expression from RNA Replicons|1|0||
|Proposed Data Model for the Next Version of the Synthetic Biology Open Language|4|4|:star:|
|Distributed Classifier Based on Genetically Engineered Bacterial Cell Cultures|2|0||

## February

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|A Synthetic Anhydrotetracycline-Controllable Gene Expression System in Ralstonia eutropha H16|4|4|:star:|
|Noise Propagation in Synthetic Gene Circuits for Metabolic Control|1|0||
Expand All @@ -42,7 +42,7 @@ header:

## March

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|RADOM, an Efficient In Vivo Method for Assembling Designed DNA Fragments up to 10 kb Long in Saccharomyces cerevisiae|4|0||
|Avoidance of Truncated Proteins from Unintended Ribosome Binding Sites within Heterologous Protein Coding Sequences|1|0||
Expand All @@ -52,7 +52,7 @@ header:

## April

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Rapid Evaluation of Tyrosine Kinase Activity of Membrane-Integrated Human Epidermal Growth Factor Receptor Using the Yeast Gγ Recruitment System|1|0||
|A Set of Versatile Brick Vectors and Promoters for the Assembly, Expression, and Integration of Synthetic Operons in Methylobacterium extorquens AM1 and Other Alphaproteobacteria|1|0||
Expand All @@ -61,7 +61,7 @@ header:

## May

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Rapidly Characterizing the Fast Dynamics of RNA Genetic Circuitry with Cell-Free Transcription–Translation (TX-TL) Systems|6|6|:star:|
|Synthetic Tunable Amplifying Buffer Circuit in E. coli|2|0||
Expand All @@ -70,51 +70,51 @@ header:

## June

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Accurate Predictions of Genetic Circuit Behavior from Part Characterization and Modular Composition|4|0||
|Expansion of Bisindole Biosynthetic Pathways by Combinatorial Construction|1|0||
|Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems|1|0||

## July

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|BASIC: A New Biopart Assembly Standard for Idempotent Cloning Provides Accurate, Single-Tier DNA Assembly for Synthetic Biology|1|1|:star:|
|Rationally Designed MicroRNA-Based Genetic Classifiers Target Specific Neurons in the Brain|1|0||
|Enhancing Bidirectional Electron Transfer of Shewanella oneidensis by a Synthetic Flavin Pathway|1|1|:star:|

## August

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Generating Systems Biology Markup Language Models from the Synthetic Biology Open Language|3|3|:star:|
|Genome Calligrapher: A Web Tool for Refactoring Bacterial Genome Sequences for de Novo DNA Synthesis|1|0||

## September

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Enhanced Protein Production in Escherichia coli by Optimization of Cloning Scars at the Vector–Coding Sequence Junction|1|0||
|Regulation of Bacterial Gene Expression by Protease-Alleviated Spatial Sequestration (PASS)|4|0||

## October

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Enzymatic Menthol Production: One-Pot Approach Using Engineered Escherichia coli|1|0||

## November

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Genome Engineering of the 2,3-Butanediol Biosynthetic Pathway for Tight Regulation in Cyanobacteria|5|4||
|A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy|1|0||
|CasEMBLR: Cas9-Facilitated Multiloci Genomic Integration of in Vivo Assembled DNA Parts in Saccharomyces cerevisiae|2|0||

## December

|Article|No. of SBOL Visual complaint images|No. of SBOL Visual images following Best practices||
|Article|No. of SBOL Visual compliant images|No. of SBOL Visual images following Best practices||
| :---: | :---: | :---: | :---: |
|Synthetic Auxotrophs with Ligand-Dependent Essential Genes for a BL21(DE3) Biosafety Strain|1|0||
|Development of a Synthetic Malonyl-CoA Sensor in Saccharomyces cerevisiae for Intracellular Metabolite Monitoring and Genetic Screening|1|0||
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