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ChassiDex: A microbial database useful for synthetic biology applications

B P, K.; D, K.; Shinde, M.; Damaraju, N.; Muthukrishnan, A. B.; Prasad, S. B.; Jayaraman, G.

2019-07-16 synthetic biology
10.1101/703033 bioRxiv
Show abstract

ChassiDex is an open-source, non-profit online host organism database that houses a repository of molecular, biological and genetic data for model organisms with applications in synthetic biology. The structured user-friendly environment makes it easy to browse information. The database consists of a page for each model organism subdivided into sections such as Growth Characteristics, Strain diversity, Culture sources, Maintenance protocol, Transformation protocol, BioBrick parts and commonly used vectors. With tools such as CUTE built for codon usage table generator, it is also easy to generate and download accurate novel codon tables for unconventional hosts in suitable formats. This database was built as a project for the International Genetically Engineered Machine Competition in 2017 with the mission of making it easy to shift from working with one host organism to another unconventional host organism for any researcher in the field of synthetic biology. The code along with other instructions for the usage of the database and tools are publicly available at the GitHub page. We encourage the synthetic biology community to contribute to the database by adding data for any additional or existing host organism.\n\nhttps://chassidex.org; https://github.com/ChassiDex

Matching journals

The top 4 journals account for 50% of the predicted probability mass.

1
ACS Synthetic Biology
● 287 papers in training set
Top 0.1%
31.5%
Similar papers in this journal
2
Nucleic Acids Research
◐ 1281 papers in training set
Top 2%
8.0%
Similar papers in this journal
3
PLOS ONE
● 5266 papers in training set
Top 22%
7.4%
Similar papers in this journal
4
Synthetic Biology
◐ 24 papers in training set
Top 0.1%
5.2%
Similar papers in this journal
50% of probability mass above
5
Metabolic Engineering Communications
○ 22 papers in training set
Top 0.1%
5.2%
Similar papers in this journal
6
PeerJ
◐ 308 papers in training set
Top 1%
4.9%
7
Biotechnology and Bioengineering
○ 53 papers in training set
Top 0.2%
3.3%
8
Frontiers in Bioengineering and Biotechnology
○ 98 papers in training set
Top 0.8%
2.2%
9
Frontiers in Microbiology
○ 427 papers in training set
Top 5%
1.9%
10
International Journal of Molecular Sciences
○ 494 papers in training set
Top 7%
1.9%
11
RSC Advances
● 22 papers in training set
Top 0.4%
1.5%
12
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 4%
1.5%
13
ACS Omega
● 105 papers in training set
Top 2%
1.4%
14
BMC Bioinformatics
○ 457 papers in training set
Top 4%
1.4%
15
Metabolic Engineering
○ 75 papers in training set
Top 0.6%
1.1%
16
G3: Genes, Genomes, Genetics
◐ 252 papers in training set
Top 3%
1.1%
17
Microbial Biotechnology
○ 34 papers in training set
Top 0.8%
0.9%
18
Genes
○ 144 papers in training set
Top 3%
0.9%
19
Microorganisms
○ 106 papers in training set
Top 3%
0.9%
20
Briefings in Bioinformatics
◐ 354 papers in training set
Top 7%
0.9%
21
BMC Biology
○ 265 papers in training set
Top 5%
0.9%
22
Synthetic and Systems Biotechnology
○ 11 papers in training set
Top 0.2%
0.9%
23
Nature Communications
○ 5641 papers in training set
Top 55%
0.9%
24
Journal of Microbiology & Biology Education
● 11 papers in training set
Top 0.1%
0.6%
25
Trends in Biotechnology
○ 12 papers in training set
Top 0.2%
0.6%
26
Advanced Science
○ 286 papers in training set
Top 10%
0.6%
27
Microbiology Spectrum
● 469 papers in training set
Top 11%
0.6%
28
Genome Biology
○ 637 papers in training set
Top 9%
0.6%
29
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 5%
0.6%
30
mSystems
● 394 papers in training set
Top 6%
0.6%

"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.