From d1968e28cd6b5ac41ef31e88b32ee1b7d59f329e Mon Sep 17 00:00:00 2001 From: Ryan Greer Date: Sun, 15 Dec 2024 14:31:23 -0700 Subject: [PATCH] changed pub type from conference paper to journal article --- content/publication/Bryce-Round-Trip-2022/index.md | 2 +- content/publication/Jones-Cello-2022/index.md | 2 +- content/publication/buecherl-tools-standards-2022/index.md | 2 +- .../publication/goldman-assessment-replication-2022/index.md | 2 +- content/publication/shaikh-biosimulators-2022/index.md | 2 +- content/publication/yu-vsearch-2022/index.md | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/content/publication/Bryce-Round-Trip-2022/index.md b/content/publication/Bryce-Round-Trip-2022/index.md index 592844716..af233e8b8 100644 --- a/content/publication/Bryce-Round-Trip-2022/index.md +++ b/content/publication/Bryce-Round-Trip-2022/index.md @@ -45,7 +45,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' abstract: Synthetic biology is a complex discipline that involves creating detailed, purpose-built designs from genetic parts. This process is often phrased as a Design-Build-Test-Learn loop, where iterative design improvements can be made, implemented, measured, and analyzed. Automation can potentially improve both the end-to-end duration of the process and the utility of data produced by the process. One of the most important considerations for the development of effective automation and quality data is a rigorous description of implicit knowledge encoded as a formal knowledge representation. The development of knowledge representation for the process poses a number of challenges, including developing effective human–machine interfaces, protecting against and repairing user error, providing flexibility for terminological mismatches, and supporting extensibility to new experimental types. We address these challenges with the DARPA SD2 Round Trip software architecture. The Round Trip is an open architecture that automates many of the key steps in the Test and Learn phases of a Design-Build-Test-Learn loop for high-throughput laboratory science. The primary contribution of the Round Trip is to assist with and otherwise automate metadata creation, curation, standardization, and linkage with experimental data. The Round Trip’s focus on metadata supports fast, automated, and replicable analysis of experiments as well as experimental situational awareness and experimental interpretability. We highlight the major software components and data representations that enable the Round Trip to speed up the design and analysis of experiments by 2 orders of magnitude over prior ad hoc methods. These contributions support a number of experimental protocols and experimental types, demonstrating the Round Trip’s breadth and extensibility. We describe both an illustrative use case using the Round Trip for an on-the-loop experimental campaign and overall contributions to reducing experimental analysis time and increasing data product volume in the SD2 program. diff --git a/content/publication/Jones-Cello-2022/index.md b/content/publication/Jones-Cello-2022/index.md index d65f32ea7..714e46fd8 100644 --- a/content/publication/Jones-Cello-2022/index.md +++ b/content/publication/Jones-Cello-2022/index.md @@ -29,7 +29,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' abstract: Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates’ structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello’s capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users’ expertise, jobs may take minutes or hours to complete. publication: '*Nature Protocols*' diff --git a/content/publication/buecherl-tools-standards-2022/index.md b/content/publication/buecherl-tools-standards-2022/index.md index 955834a56..dbb2eebda 100644 --- a/content/publication/buecherl-tools-standards-2022/index.md +++ b/content/publication/buecherl-tools-standards-2022/index.md @@ -27,7 +27,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' publication: '*Current Opinion in Microbiology*' doi: https://doi.org/10.1016/j.mib.2022.102155 diff --git a/content/publication/goldman-assessment-replication-2022/index.md b/content/publication/goldman-assessment-replication-2022/index.md index 62ed194bf..f33b32c18 100644 --- a/content/publication/goldman-assessment-replication-2022/index.md +++ b/content/publication/goldman-assessment-replication-2022/index.md @@ -61,7 +61,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' publication: '*Synthetic Biology*' doi: 10.1093/synbio/ysac018 diff --git a/content/publication/shaikh-biosimulators-2022/index.md b/content/publication/shaikh-biosimulators-2022/index.md index 8e79c9627..f951f4d35 100644 --- a/content/publication/shaikh-biosimulators-2022/index.md +++ b/content/publication/shaikh-biosimulators-2022/index.md @@ -100,7 +100,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' publication: '*Nucleic Acids Research*' doi: 10.1093/nar/gkac331 diff --git a/content/publication/yu-vsearch-2022/index.md b/content/publication/yu-vsearch-2022/index.md index 402246dd6..e9cc2e18e 100644 --- a/content/publication/yu-vsearch-2022/index.md +++ b/content/publication/yu-vsearch-2022/index.md @@ -28,7 +28,7 @@ image: # Otherwise, set `projects = []`. projects: [] publication_types: -- '1' +- '2' abstract: The ability to search for a part by its sequence is crucial for a large repository of parts. Prior to this work, however, this was not possible on SynBioHub. Sequence-based search is now integrated into SynBioHub, allowing users to find a part by a sequence provided in plain text or a supported file format. This sequence-based search feature is accessible to users via SynBioHub’s web interface, or programmatically through its API. The core implementation of the tool uses VSEARCH, an open source, global alignment search tool, and it is integrated into SBOLExplorer, an open source distributed search engine used by SynBioHub. We present a new approach to scoring part similarity using SBOLExplorer, which takes into account both the popularity and percentage match of parts. publication: '*ACS Synthetic Biology*'