Evidence map›Paper›PMID 26568632›Full record

ArticleBioinformatics (Oxford, England)2016

BioPartsBuilder: a synthetic biology tool for combinatorial assembly of biological parts.

Kun Yang, Giovanni Stracquadanio, Jingchuan Luo, Jef D Boeke, Joel S Bader

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Bioinformatics (Oxford, England), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

7 citing papers in PubMed.

  1. Biocircuits in plants and eukaryotic algae.Frontiers in plant science · 2022
    Review
  2. Review
  3. Article
  4. Article
  5. Article
  6. Review
  7. Low escape-rate genome safeguards with minimal molecular perturbation ofProceedings of the National Academy of Sciences of the United States of America · 2017
    Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Kun YangDepartment of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.
Giovanni StracquadanioDepartment of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.
Jingchuan LuoInstitute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA.
Jef D BoekeInstitute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, NYU Langone Medical Center, New York, NY 10016, USA.
Joel S BaderDepartment of Biomedical Engineering, Johns Hopkins University, 3400 N. Charles Street, Baltimore, MD 21218, USA and.

Funding

Training CoreP50GM107632 · NIGMS · NEW YORK UNIVERSITY SCHOOL OF MEDICINE · PI BURNS, KATHLEEN H · 2013 to 2017
$10.0M
NIGMS NIH HHS P50 GM107632
6 · The paper itself

Abstract

unlabelledCombinatorial assembly of DNA elements is an efficient method for building large-scale synthetic pathways from standardized, reusable components. These methods are particularly useful because they enable assembly of multiple DNA fragments in one reaction, at the cost of requiring that each fragment satisfies design constraints. We developed BioPartsBuilder as a biologist-friendly web tool to design biological parts that are compatible with DNA combinatorial assembly methods, such as Golden Gate and related methods. It retrieves biological sequences, enforces compliance with assembly design standards and provides a fabrication plan for each fragment. AVAILABILITY AND IMPLEMENTATION: BioPartsBuilder is accessible at http://public.biopartsbuilder.org and an Amazon Web Services image is available from the AWS Market Place (AMI ID: ami-508acf38). Source code is released under the MIT license, and available for download at https://github.com/baderzone/biopartsbuilder CONTACT: joel.bader@jhu.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Indexed as

Synthetic BiologyDNAProgramming LanguagesDNA

Identifiers

PMID26568632
PMCPMC4803390

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.