Back

GenIE-Sys: Genome Integrative Explorer System

Mannapperuma, C.; Waterworth, J.; Street, N.

2019-10-17 bioinformatics
10.1101/808881 bioRxiv
Show abstract

There are an ever-increasing number of genomes being sequenced, many of which have associated RNA sequencing and other genomics data. The availability of user-friendly web-accessible mining tools ensures that these data repositories provide maximum benefit to the community. However, there are relatively few options available for setting up such standalone frameworks. We developed the Genome Integrative Explorer System (GenIE-Sys) to set up web resources to enable search, visualization and exploration of genomics data typically generated by a genome project.\n\nGenIE-Sys is implemented in PHP, JavaScript and Python and is freely available under the GNU GPL 3 public license. All source code is freely available at the GenIE-Sys website (https://geniesys.org) or GitHub (http://github.com/plantgenie/geniesys.git). Documentation is available at http://geniesys.readthedocs.io.

Matching journals

The top 6 journals account for 50% of the predicted probability mass.

1
Database
◐ 61 papers in training set
Top 0.1%
12.5%
Similar papers in this journal
2
PLOS ONE
● 5266 papers in training set
Top 16%
11.7%
Similar papers in this journal
3
BMC Bioinformatics
○ 457 papers in training set
Top 0.5%
11.7%
Similar papers in this journal
4
GigaScience
◐ 212 papers in training set
Top 0.3%
6.6%
Similar papers in this journal
5
NAR Genomics and Bioinformatics
◐ 242 papers in training set
Top 0.7%
5.5%
Similar papers in this journal
6
Plant Methods
○ 42 papers in training set
Top 0.1%
5.5%
50% of probability mass above
7
Bioinformatics
◐ 1204 papers in training set
Top 4%
5.4%
8
BMC Research Notes
○ 33 papers in training set
Top 0.1%
4.3%
9
Nucleic Acids Research
◐ 1281 papers in training set
Top 5%
4.0%
10
Gigabyte
● 62 papers in training set
Top 0.4%
2.4%
11
G3 Genes|Genomes|Genetics
◐ 351 papers in training set
Top 2%
2.4%
12
F1000Research
○ 88 papers in training set
Top 0.8%
2.4%
13
Bioinformatics Advances
◐ 203 papers in training set
Top 3%
2.1%
14
Journal of Bioinformatics and Systems Biology
○ 15 papers in training set
Top 0.1%
2.1%
15
BMC Genomics
○ 406 papers in training set
Top 4%
1.7%
16
Frontiers in Plant Science
○ 256 papers in training set
Top 4%
1.1%
17
PeerJ
◐ 308 papers in training set
Top 8%
1.1%
18
Briefings in Bioinformatics
◐ 354 papers in training set
Top 6%
1.1%
19
Plant Physiology
◐ 238 papers in training set
Top 2%
1.1%
20
Scientific Reports
○ 3612 papers in training set
Top 67%
1.0%
21
Plant Direct
○ 95 papers in training set
Top 2%
1.0%
22
Frontiers in Genetics
○ 230 papers in training set
Top 6%
0.8%
23
Applications in Plant Sciences
○ 23 papers in training set
Top 0.4%
0.8%
24
Computational and Structural Biotechnology Journal
● 242 papers in training set
Top 7%
0.8%
25
Genes
○ 144 papers in training set
Top 4%
0.8%
26
SoftwareX
○ 15 papers in training set
Top 0.4%
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.