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View Code? Open in Web Editor NEWWebsite for global antimicrobial peptides.
Home Page: https://ampsphere.big-data-biology.org/home
License: MIT License
Website for global antimicrobial peptides.
Home Page: https://ampsphere.big-data-biology.org/home
License: MIT License
Is your feature request related to a problem? Please describe.
Yeah, to delete text search bar for a while, we need a new layout.
Describe the solution you'd like
Maybe something like
<div class="row">
<div class="q-col-md-1 q-col-12"></div> # for the logo
<div class="q-col-md-11 q-col-12"></div> # for the mavigation bar, maybe remove the bg color to make it clearer.
</div>
calling it 'microbial host' seems better
+ implement a column and the filter in the browser tab for the AMP taxon origin (ex. E. coli)
+ implement file format and columns explanation in the download page
+ add more explanation in the independent and conditional e-values in the HMMer search page (Family search)
HMM logos are currently PNGs, but they clearly should be SVGs.
Is your feature request related to a problem? Please describe.
Filter by the microbial source isn't practical enough.
Describe the solution you'd like
Change microbial sources to adopt GTDB taxonomic classification tree.
Describe alternatives you've considered
No
Additional context
Helpful resource:
Database statistics for the home page are very slow when calculation, this should be accelerated by create a statistics table in the database. Also, API will directly retrieve the data from the table, not real-timely calculate using all data in the database.
Automatically fit the content of each page to the window size.
https://plotly.com/python/distplot/
--- curve distplots where we have AMPSphere curve, family curve, and an array pointing to the site of the current AMP should be.
This is a bug, causing empty distribution graphs on the amp page.
Example: AMP10.007_686 and AMP10.000_732
Use opacity
of graph data and centered text to display empty graph.
Describe the bug
Downloading sphere files results in a redirect to 127.0.0.1 (which then fails).
To Reproduce
Steps to reproduce the behavior:
Downloads
tabExpected behavior
Download a file
Desktop (please complete the following information):
Chrome on Linux
#!/usr/bin/env python
import sys
from Bio import AlignIO
from Bio.Align import AlignInfo
alignment = AlignIO.read(sys.argv[1], 'fasta')
summary_align = AlignInfo.SummaryInfo(alignment)
summary_align.dumb_consensus(float(sys.argv[2]))
Is your feature request related to a problem? Please describe.
The current design is confusing: it is not clear to the user what these features are.
Describe the solution you'd like
A single search box, but two output tabs.
Is your feature request related to a problem? Please describe.
Right now, the Download tab is empty for families with fewer than 8 elements. At least the sequences FASTA can be provided.
The information is there (the sequences are displayed already), the file can even be generated in JS.
Change the behavior of get_page_info
function in crud.py
.
def get_page_info(kind: str, page_size: int, page: int, db: Session,
accession: str = None, search_text: str = None):
if kind == 'amp':
total_items = db.query(models.AMP.accession).count()
https://ampsphere.big-data-biology.org/home
Everytime you cycle, a counter gets incremented. Also, clicking OK once should make the warning go away forever.
Use https://shields.io/ or https://badgen.net/ to generate the badges.
Reference colors:
Potential icon resources: https://www.g2.com/products/biorender/competitors/alternatives
General information
disordered
)air 3681
anthropogenic 4055
anthropogenic:built environment 21418
anthropogenic:food 7
anthropogenic:food:fermented food 1848
anthropogenic:mine 555
anthropogenic:mock community 106
anthropogenic:sludge 33206
anthropogenic:wastewater 39952
aquatic 2093
aquatic:estuarine 4521
aquatic:freshwater 55769
aquatic:freshwater:lake 31024
aquatic:freshwater:pond 458
aquatic:freshwater:river 13313
aquatic:groundwater 7670
aquatic:ice 3214
aquatic:marine 96479
aquatic:marine:pelagic 43051
aquatic:saline 19152
aquatic:spring:hot spring 2304
aquatic:spring:hydrothermal vent 1523
host-associated:algal host 232
host-associated:animal host 19063
host-associated:animal host:coral reef 3407
host-associated:animal host:digestive tract 654
host-associated:animal host:digestive tract:intestine 218637
host-associated:animal host:digestive tract:mouth 11402
host-associated:animal host:digestive tract:mouth:saliva 7458
host-associated:animal host:digestive tract:rumen 41552
host-associated:animal host:insect host 2854
host-associated:animal host:mammalian host:human host 271
host-associated:animal host:reproductive tract 197
host-associated:animal host:respiratory tract 3377
host-associated:animal host:skin 6535
host-associated:animal host:urogenital tract 109
host-associated:plant host 6249
host-associated:plant host:leaf 2993
host-associated:plant host:phyllosphere 5264
host-associated:plant host:plant litter 9896
host-associated:plant host:rhizosphere 75929
nan 4094
ph:alkaline 1514
sediment 51020
terrestrial 4116
terrestrial:dust 50
terrestrial:halite 326
terrestrial:permafrost 9048
terrestrial:soil 240668
terrestrial:subsurface 1806
terrestrial:wetland 20207
Is your feature request related to a problem? Please describe.
For example, the page
https://ampsphere.big-data-biology.org/family?accession=SPHERE-III.003_141
could have the logo
Describe the solution you'd like
See the logo.
Description
The CSV downloaded from the Browse page is unnecessarily large and the format is not CSV-friendly at all. Maybe selecting just some of the columns and the sequences per page makes a better result, or at least, provides a more readily parsed file.
To Reproduce
Steps to reproduce the behavior:
Expected behavior
A better format for the CSV file, easier to parse, and virtually smaller in size.
Desktop (please complete the following information):
Using the command below will accelerate mmseqs search by a factor of 100, and can avoid timeout when waiting for search response.
mmseqs createdb AMPSphere_v.2021-03.faa AMPSphere_v.2021-03.mmseqsdb
mmseqs createindex AMPSphere_v.2021-03.mmseqsdb tmp
mmseqs createdb input.fasta input.mmseqsdb && \
mmseqs search input.mmseqsdb AMPSphere_v.2021-03.mmseqsdb search_results.mmseqsdb tmp && \
mmseqs createtsv input.mmseqsdb AMPSphere_v.2021-03.mmseqsdb search_results.mmseqsdb search_results.tsv
Is your feature request related to a problem? Please describe.
Currently, the package size is too large and makes the website a bit slow.
Describe the solution you'd like
Can be improved by importing Quasar through CDN (https://quasar.dev/start/umd).
Describe alternatives you've considered
No
Additional context
No
Describe the bug
HMM logo images are incomplete?
To Reproduce
Desktop (please complete the following information):
Chrome on Linux, but I see the error with wget
/curl
too
From Biopython documentation (https://biopython.org/docs/1.76/api/Bio.SeqUtils.ProtParam.html), I noticed that the three probabilities of the helix, turn and sheet are independent. There is one amido acid 'L' that can involve in both helix and sheet. So, we cannot treat the resting probability as 'disordered'.
The secondary structure pie chart and error bars chart should be changed.
The current layout is based on Quasar but changing all Element Plus components is too costly. Leave this here for following up when other important tasks are done.
So far I have tried but had no success.
(base) huichong@ip-172-31-43-121:~/projects/caddy-learn$ sudo caddy run │··································
[sudo] password for huichong: │··································
2021/11/30 10:49:53.039 INFO using adjacent Caddyfile │··································
2021/11/30 10:49:53.040 INFO admin admin endpoint started {"address": "tcp/localhost:2019", "enforce_origin": false, "origins": ["localhost:2019", "[::1]:2019", "127│··································
.0.0.1:2019"]} │··································
2021/11/30 10:49:53.040 INFO http server is listening only on the HTTPS port but has no TLS connection policies; adding one to enable TLS {"server_name": "srv0", "ht│··································
tps_port": 443} │··································
2021/11/30 10:49:53.040 INFO http enabling automatic HTTP->HTTPS redirects {"server_name": "srv0"} │··································
2021/11/30 10:49:53.041 INFO http enabling automatic TLS certificate management {"domains": ["huichong.me"]} │··································
2021/11/30 10:49:53.057 INFO tls.cache.maintenance started background certificate maintenance {"cache": "0xc000340af0"} │··································
2021/11/30 10:49:53.058 INFO tls cleaning storage unit {"description": "FileStorage:/root/.local/share/caddy"} │··································
2021/11/30 10:49:53.061 INFO tls finished cleaning storage units │··································
2021/11/30 10:49:53.427 INFO autosaved config (load with --resume flag) {"file": "/root/.config/caddy/autosave.json"} │··································
2021/11/30 10:49:53.427 INFO serving initial configuration
huichong.me
as a test domain(base) huichong@ip-172-31-43-121:~/projects/caddy-learn$ sudo certbot certonly --nginx │··································
Saving debug log to /var/log/letsencrypt/letsencrypt.log │··································
Please enter the domain name(s) you would like on your certificate (comma and/or │··································
space separated) (Enter 'c' to cancel): huichong.me │··································
Requesting a certificate for huichong.me │··································
│··································
Certbot failed to authenticate some domains (authenticator: nginx). The Certificate Authority reported these problems: │··································
Domain: huichong.me │··································
Type: unauthorized │··································
Detail: Invalid response from http://huichong.me/.well-known/acme-challenge/Z53Fx14Ma4rbAXW9VDO8FbqNehgcJOIBx5Jzus4A-I4 [185.199.111.153]: "<!DOCTYPE html>\n<html>\n <h│··································
ead>\n <meta http-equiv=\"Content-type\" content=\"text/html; charset=utf-8\">\n <meta http-equiv=\"Co" │··································
│··································
Hint: The Certificate Authority failed to verify the temporary nginx configuration changes made by Certbot. Ensure the listed domains point to this nginx server and that i│··································
t is accessible from the internet. │··································
│··································
Some challenges have failed. │··································
Ask for help or search for solutions at https://community.letsencrypt.org. See the logfile /var/log/letsencrypt/letsencrypt.log or re-run Certbot with -v for more details.
This will eat a lot of time. I cannot estimate how much. Any ideas?
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