What is SSAM-lite?
--
-
WEBAPp
-runs only in Browser
-SSAM paper etc
-
SSAM-lite is a lightweight, browser-based implementation of the SSAM framework. +It provides the functionality of SSAMs most popular and widely used features in a graphical user interface +with a few functions added for convenience and ease of use.
+TODO what does SSAM do
Citations
TODO please correct me!
@@ -86,7 +85,24 @@Citations
License
-TODO enter license here
+TODO do we stick to the MIT license
+MIT License
+Copyright (c) 2021 sebastiantiesmeyer
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the “Software”), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+THE SOFTWARE IS PROVIDED “AS IS”, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.
Contents:
@@ -105,6 +121,7 @@ LicenseTutorial
- Usage
- Open SSAM-lite
+- Navigation
- Data
- Parameters
- Analysis
diff --git a/docs/build/html/quickstart.html b/docs/build/html/quickstart.html
index a3bb447..5694117 100644
--- a/docs/build/html/quickstart.html
+++ b/docs/build/html/quickstart.html
@@ -94,11 +94,12 @@ Test data
My first analysis
-Open the index.html from the directory you just unzipped.
+Open the index.html from the unzipped SSAM-lite directory by double-clicking.
Click on Get going!
-Click on “coordinates” and select the coordinates.csv from the sample data.
-Do the same for the “signatures” (obviously use the signature.csv this time, duh!)
-Time is flying by so we skip the “Parameters” section heading straight for “Analysis” and click on “Run Kernel Density Estimation”.
+
Click on “Coordinates” and select the coordinates.csv from the sample data.
+Do the same for the “Signatures” (obviously use the signature.csv this time, duh!)
+Time is flying by so we skip the “Parameters” section, leaving them at their default values,
+heading straight for “Analysis” and click on “Run Kernel Density Estimation”.
Time for a short break now, this step might take 2 mins.
When the KDE has been estimated scroll further down and hit “Infer Cell Types”. Done!
That’s how easy SSAM-lite is!
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js
index 2a7c8d2..2f4b4c7 100644
--- a/docs/build/html/searchindex.js
+++ b/docs/build/html/searchindex.js
@@ -1 +1 @@
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diff --git a/docs/build/html/tutorial.html b/docs/build/html/tutorial.html
index 22ab000..ae725d7 100644
--- a/docs/build/html/tutorial.html
+++ b/docs/build/html/tutorial.html
@@ -72,7 +72,9 @@
Tutorial
-refernce tutorial in app
+TODO do we need a tutorial? there is not a lot of room between the quickstart and the usage anyway?
+After installation of SSAM-lite, this tutorial will help you get to
+know the basic workflow of
diff --git a/docs/build/html/usage.html b/docs/build/html/usage.html
index 14ded20..f1b1d8f 100644
--- a/docs/build/html/usage.html
+++ b/docs/build/html/usage.html
@@ -48,6 +48,7 @@
- SSAM-lite-server
+- Navigation
- Data
- Parameters
- Analysis
@@ -96,19 +97,29 @@ SSAM-lite-solo
SSAM-lite-server
-To connet to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
+
To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000).
-However, the IP and port depends on your local setup. Talk to your SSAM-lite coordinator.
+However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.
+
Data
-To be able to use SSAM-lite you need to prepare your data in csv format.
-Two input files are required:
+The Data will be uploaded in the Data Center section of the tool. By clicking the “Coordinates”
+or “Signatures” button and selecting the correct files.
+To be able to use SSAM-lite you need to prepare your data in csv format.
+Two input files are required and must be structured as follows:
- mRNA Coordinates
This file needs to be of the form Gene, x-coordinate, y-coordinate.
The name of the headers are irrelevant, however their order needs to be kept.
-Negative coordinates are possible.
+Negative coordinates are possible and the units do not matter. However, their magnitude
+might have an influence on proper parameter values later on.
Contents:
-
@@ -105,6 +121,7 @@
- Usage
- Open SSAM-lite +
- Navigation
- Data
- Parameters
- Analysis diff --git a/docs/build/html/quickstart.html b/docs/build/html/quickstart.html index a3bb447..5694117 100644 --- a/docs/build/html/quickstart.html +++ b/docs/build/html/quickstart.html @@ -94,11 +94,12 @@
- SSAM-lite-server
Test data
My first analysis
-Open the index.html from the directory you just unzipped.
+Open the index.html from the unzipped SSAM-lite directory by double-clicking.
Click on Get going!
-Click on “coordinates” and select the coordinates.csv from the sample data. -Do the same for the “signatures” (obviously use the signature.csv this time, duh!)
-Time is flying by so we skip the “Parameters” section heading straight for “Analysis” and click on “Run Kernel Density Estimation”. +
Click on “Coordinates” and select the coordinates.csv from the sample data. +Do the same for the “Signatures” (obviously use the signature.csv this time, duh!)
+Time is flying by so we skip the “Parameters” section, leaving them at their default values, +heading straight for “Analysis” and click on “Run Kernel Density Estimation”. Time for a short break now, this step might take 2 mins.
When the KDE has been estimated scroll further down and hit “Infer Cell Types”. Done!
That’s how easy SSAM-lite is!
diff --git a/docs/build/html/searchindex.js b/docs/build/html/searchindex.js index 2a7c8d2..2f4b4c7 100644 --- a/docs/build/html/searchindex.js +++ b/docs/build/html/searchindex.js @@ -1 +1 @@ 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-refernce tutorial in app
+TODO do we need a tutorial? there is not a lot of room between the quickstart and the usage anyway?
+After installation of SSAM-lite, this tutorial will help you get to +know the basic workflow of
+ - Navigation
- Data
- Parameters
- Analysis @@ -96,19 +97,29 @@
- mRNA Coordinates
This file needs to be of the form Gene, x-coordinate, y-coordinate. The name of the headers are irrelevant, however their order needs to be kept. -Negative coordinates are possible.
+Negative coordinates are possible and the units do not matter. However, their magnitude +might have an influence on proper parameter values later on.
LicenseTutorial
SSAM-lite-solo
SSAM-lite-server
-To connet to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
+
To connect to SSAM-lite-server, you will need to to open your favourite Web Browser (not IE)
and enter the correct IP address and port in the form {ip}:{port} (e.g. 127.0.0.1:5000).
-However, the IP and port depends on your local setup. Talk to your SSAM-lite coordinator.
+However, the IP and port depends on your local setup. Talk to your responsible SSAM-lite coordinator.
+
Data
-To be able to use SSAM-lite you need to prepare your data in csv format.
-Two input files are required:
+The Data will be uploaded in the Data Center section of the tool. By clicking the “Coordinates”
+or “Signatures” button and selecting the correct files.
+To be able to use SSAM-lite you need to prepare your data in csv format.
+Two input files are required and must be structured as follows:
Data
-To be able to use SSAM-lite you need to prepare your data in csv format.
-Two input files are required:
+The Data will be uploaded in the Data Center section of the tool. By clicking the “Coordinates” +or “Signatures” button and selecting the correct files. +To be able to use SSAM-lite you need to prepare your data in csv format. +Two input files are required and must be structured as follows:
