AMaSS (Adelson Mass Spec System) is a web site for distributing and analyzing results from mass spectrometry experiments. AMaSS is implemented using jQuery, bootstrap, and bootgrid, and plot.ly.
AMaSS is designed to support multiple types of experiment results. Currently, analysis is only available for abundance-type experiments (e.g., label-free peptide counting and BioID screening). Users may normalize results from multiple runs (replicates), calculate differential abundance among runs, and visualize these results as violin plots, heatmaps, or volcano plots. Data for all types of experiments (e.g., abundance, generic) may be downloaded in the original upload format (typically as Excel spreadsheets) or as tab-separated-value (TSV) files if AMaSS can parse the data set.
(Note: Only "important" files are listed.)
AMaSS/
├── cgi-bin/ (Contains CGI scripts detailed later)
│ ├── frontpage.py (Main CGI script called by web site home page)
│ └── amass_lib (Python library for parsing and saving data sets)
├── experiments/
│ ├── raw/ (Contains raw data files for later downloading)
│ ├── cooked/ (Contains parsed data files)
│ └── index.json (Contains data set metadata)
└── html/ (Contains all files served directly to the user)
├── js/ (Contains all pertinent JS files)
│ ├── frontpage.js (Main JS code for front page)
│ └── fp-*.js (Per-experiment-type and support JS)
├── css/ (Contains all pertinent CSS files)
│ └── frontpage.css (Main CSS code for front page)
├── icons/ (Contains images for use as icons)
├── frontpage.html (Main web page for users accessing data sets)
├── upload.html (Main web page for users uploading data sets)
└── index.html (symlink to frontpage.html)
index.html and upload.html are both symlinks to frontpage.html.
index.html is present so users do not need to include "frontpage.html"
in their URL. upload.html deletes the "Upload" tab on load, but
behaves identically to frontpage.html otherwise.
Changelog is not at all comprehensive, more specific changes can be found in previous GitHub commits.
* v0.1 (June 3, 2019)
* Reimplemented using Bootstrap and Bootgrid as main Javascript
libraries.
* Support new upload data format.
* Renamed from MSWeb to AMaSS.
* v0.0.3 (September 8, 2018)
* Changes JSON metadata format to add entries for number of columns
and rows in each data set, as well as adding columns in experiment
table to accommodate changed format.
* Moves list of selected experiments to status box below experiment table.
* Removes select button from experiment table, functionality shifted
to user being able to click a row to select it.
* v0.0.2 (09/1/2018)
* Adds functions to select and deselect experiments in table,
retrieve title of data set from hash, and updating selected
experiments in selected
* v0.0.1 (08/31/2018)
* Moved all previous files in html/ to html_old/.
* Adds new index.html to html/, adds west.js/center.js/init.js,
sets up 2-paned layout in jQuery UI, imports important library
files from html_old.
* Changes format of metadata to add explicit keys for
uploader/upload date and experiment date/type/conditions.
* Changes JSON indexing to use OrderedDict to create metadata in JSON file.
* Adds functions to populate experiment table with data sets from index.json
* Pre v0.0.1 (08/01/2018-08/30/2018)
* MSWeb initial layout. (Files found in html_old) Page now set up
with jQuery/jQuery UI. Comprised of three main layout containers
(west, center, and south). West container contains title,
search bar, and experiment filters. Experiments are shown in
jQuery multiselect box and basic plotting completed in south div,
as well as initial implementation of react-chart-editor.
* Initial Stage (06/26/2018-07/30/2018)
* Tool in its most basic form. Entire page initially created
with basic HTML/JavaScript and eventually partially in React.
Tool has basic framework for data parsing and retrieval,
but plotting is limited to basic plot.ly plotting.