A web app for recoding genes by organism.
See the deployment at basebuddy.lbl.gov.
If you use this tool, please cite the BaseBuddy paper (Schmidt et al. 2023) and DnaChisel:
Matthias Schmidt, Namil Lee, Chunjun Zhan, Jacob B. Roberts, Alberto A. Nava, Leah S. Keiser, Aaron A. Vilchez, Yan Chen, Christopher J. Petzold, Robert W. Haushalter, Lars M. Blank, and Jay D. Keasling ACS Synthetic Biology 2023 12 (11), 3366-3380, https://doi.org/10.1021/acssynbio.3c00367
Valentin Zulkower, Susan Rosser, DNA Chisel, a versatile sequence optimizer, Bioinformatics, Volume 36, Issue 16, August 2020, Pages 4508–4509, https://doi.org/10.1093/bioinformatics/btaa558.
- Clone the repo:
git clone git@github.com:JBEI/basebuddy.git - Decompress the cocoput table:
cd data && tar -xvf cocoput_table.tsv.tar.gz && cd .. - Run streamlit in docker:
bash run_locally.sh
BaseBuddy utilizes many separate libraries and packages including:
We thank all their contributors and maintainers!
Use of the third-party software, libraries or code BaseBuddy may be governed by separate terms and conditions or license provisions. Your use of the third-party software, libraries or code is subject to any such terms and you should check that you can comply with any applicable restrictions or terms and conditions before use.
BaseBuddy is distributed under a modified BSD license (see LICENSE).
BaseBuddy Copyright (c) 2023, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy) and University of California, Berkeley. All rights reserved.
If you have questions about your rights to use or distribute this software, please contact Berkeley Lab's Intellectual Property Office at IPO@lbl.gov.
NOTICE. This Software was developed under funding from the U.S. Department of Energy and the U.S. Government consequently retains certain rights. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, distribute copies to the public, prepare derivative works, and perform publicly and display publicly, and to permit others to do so.