Merge remote-tracking branch 'origin/master'

CITATION.cff

@@ -0,0 +1,42 @@
+cff-version: 1.2.0
+message: "If you use this software, please cite it as below."
+authors:
+  - family-names: "Smit"
+    given-names: "Jochem H."
+    orcid: "https://orcid.org/0000-0002-3597-9429"
+title: "PyHDX"
+version: 0.4.0b5
+doi: 10.5281/zenodo.4062031
+date-released: 2021-12-01
+url: "https://github.com/Jhsmit/PyHDX"
+preferred-citation:
+  type: article
+  authors:
+    - family-names: "Smit"
+      given-names: "Jochem H."
+      orcid: "https://orcid.org/0000-0002-3597-9429"
+    - family-names: "Krishnamurthy"
+      given-names: "Srinath"
+      orcid: "https://orcid.org/0000-0001-5492-4450"
+    - family-names: "Srinivasu"
+      given-names: "Bindu Y."
+      orcid: "https://orcid.org/0000-0003-0875-2680"
+    - family-names: "Parakra"
+      given-names: "Rinky"
+      orcid: "https://orcid.org/0000-0001-8690-7073"
+    - family-names: "Karamanou"
+      given-names: "Spyridoula"
+      orcid: "https://orcid.org/0000-0002-8803-1404"
+    - family-names: "Economou"
+      given-names: "Anastassios"
+      orcid: "https://orcid.org/0000-0002-1770-507X"
+  doi: "10.1021/acs.analchem.1c02155"
+  journal: "Analytical Chemistry"
+  month: 9
+  start: 12840 # First page number
+  end: 12847 # Last page number
+  title: "Probing Universal Protein Dynamics Using Hydrogen–Deuterium Exchange Mass Spectrometry-Derived Residue-Level Gibbs Free Energy"
+  number: 38
+  volume: 93
+  year: 2021
+  url: "https://doi.org/10.1021/acs.analchem.1c02155"

README.rst

@@ -27,7 +27,7 @@ PyHDX
 
 .. raw:: html
 
-    <img src="images/PyHDX_rgb.png" width="1000" />
+    <img src="images/screenshot_pyhdx040b5.png" width="1000" />
 
 
 PyHDX is python project which can be used to derive Gibbs free energy from HDX-MS data.
@@ -63,22 +63,17 @@ http://pyhdx.jhsmit.org/main
 
 A test file can be downloaded from `here <https://raw.githubusercontent.com/Jhsmit/PyHDX/master/tests/test_data/ecSecB_apo.csv>`_ and `here <https://raw.githubusercontent.com/Jhsmit/PyHDX/master/tests/test_data/ecSecB_dimer.csv>`_. (right click, save as).
 
-Two other web applications are available.
-To upload fitting results from the main application and visualize: 
-http://pyhdx.jhsmit.org/single
-
-To upload multiple fitting result datasets and compare and visualize:
-http://pyhdx.jhsmit.org/diff
-
-The 0.4.0b1 version of PyHDX (featuring batch fitting / multiple states) is hosted at:
+The 0.4.0b4 version of PyHDX (featuring batch fitting / multiple states) is hosted at:
 http://pyhdx-beta.jhsmit.org/main
 
 The latest beta docs are found `here <https://pyhdx.readthedocs.io/en/latest/>`_
 
-BioRxiv paper
-=============
+Publication
+===========
+
+Our Analytical Chemistry Publication describing PyHDX can be found here: https://doi.org/10.1021/acs.analchem.1c02155
 
-The latest version (v2) of our biorxiv paper can be found here: https://doi.org/10.1101/2020.09.30.320887 
+The latest version (v2) of our biorxiv paper: https://doi.org/10.1101/2020.09.30.320887 
 
 Python code for analysis and generation the figures in the paper are here: https://github.com/Jhsmit/PyHDX-paper