Merge pull request #37 from MobleyLab/submission_link

Add host-guest submission instructions and url

README.md

@@ -15,7 +15,7 @@ Join our [SAMPL7 e-mail list](http://eepurl.com/gpBBun) to get e-mails with SAMP
 - Final information on the Gibb octa acid-based challenge ("Gibb deep cavity cavitand" (GDCC) challenge) in the `host_guest/GDCC_and_guests` directory.
 - Final information on the cyclodextrin derivatives challenge in the `host_guest/cyclodextrin_derivatives` directory and in our [host-guest challenge description](host_guest_description.md).
 - Experimental details for the CD challenge in [host_guest_description.md](host_guest_description.md)
-- [Host-guest participation instructions](host_guest_instructions.md) with information on the submission format, etc. Our submission upload system is still being prepared. Submission formats are available in the subdirectories for the individual host-guest systems.
+- [Host-guest participation instructions](host_guest_instructions.md) with information on the submission format, etc. Our submission system is also [now available](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/). Submission formats are available in the subdirectories for the individual host-guest systems.
 
 All three host-guest components of this challenge are now final and launched, though additional supporting files may be added at a later date. **The submission deadline is Oct. 1 for the TrimerTrip host-guest challenge and Nov. 1 for the cyclodextrin derivatives and GDCC challenges**, due to timescales for data collection and publication of the experimental data.
 
@@ -39,6 +39,7 @@ All three host-guest components of this challenge are now final and launched, th
 - Added host-guest submission template files and instructions (Sept. 18, 2019)
 - Made more clear which compounds/cases are optional (Sept. 23, 2019)
 - Make clear that free energy predictions (and uncertainties) are required; enthalpies optional (Sept. 23, 2019)
+- Add links to [host-guest submission system](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/)
 
 ## Challenge overview
 

host_guest/GDCC_and_guests/README.md

@@ -45,7 +45,7 @@ The protonation state of the host may in some cases be not completely certain, a
 - Hosts: `host_files`: Folder containing PDB, MOL2 and SDF files for the Octa Acid (OA) host and the exo-OA host. Contains the the jupyter notebook used to generate the MOL2 and SDF files of the guests.
 - Guests: `guest_files`: Folder containing files for the eight guests, SMILES strings, and the jupyter notebook used to generate PDB, MOL2 and SDF files of the guests.
 - Images: `images`: Folder containing images of the guest and host structures for this challenge in PDF format.
-- Submission format: `GDCC_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system.
+- Submission format: `GDCC_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system. Visit [host_guest_instructions.md](../host_guest_instructions.md) for submission instructions.
 
 **Source files**:
 For this portion of the challenge, the original source files were two (provided) host PDB files from Paolo Suating (in the `host_files` directory) and a `SAMPL7_guests.cdx` file from Bruce Gibb (in the `guest_files` directory). All other files here were derived from those files.

host_guest/Isaacs_clip/README.md

@@ -20,7 +20,7 @@ Note that we have typically selected reasonable protonation states and conformer
 - Hosts: `host_files`: Folder containing PDB, MOL2, SDF and Chemdraw files for the TrimerTrip host. Contains a detailed description of input file generation for the TrimerTrip host.
 - Guests: `guest_files`: Folder containing files for the 15 guests, SMILES strings, and the jupyter notebook used to generate PDB, MOL2 and SDF files of the guests.
 - Images: `images`: Folder containing an image of the guest and host structures for this challenge in JPG file format.
-- Submission format: `Clip_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system.
+- Submission format: `Clip_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system. Visit [host_guest_instructions.md](../host_guest_instructions.md) for submission instructions.
 
 **Source files**
 In this case the original source files provided were:

host_guest/cyclodextrin_derivatives/README.md

@@ -39,7 +39,7 @@ Note that we have typically selected reasonable protonation states and conformer
 - Hosts: `host_files`: Folder containing beta cyclodextrin plus the eight other cyclodextrin derivative hosts, provided by Katy Kellett and Michael Gilson, initially only in PDB format with all protons present. The Chemdraw files are also provided. MOL2 and SDF files of the hosts were added on 7/18/19.
 - Guests: `guest_files`: Contains MOL2, PDB and SDF files and files containing the isomeric SMILES strings and codenames of the guests.
 - Images: `images`: Folder containing images of the guest and host structures for this challenge in JPG and PDF format.
-- Submission format: `CD_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system.
+- Submission format: `CD_submission.txt`: Example submission file (please replace the text and values with your own!) for submitting to our system. Visit [host_guest_instructions.md](../host_guest_instructions.md) for submission instructions.
 
 **Source files**:
 - PDB files of all hosts from the Gilson lab, which served to generate host sdf and mol2 files

host_guest_instructions.md

@@ -52,7 +52,9 @@ All hosts and guests are provided in mol2, PDB and SDfile formats. A README.md f
 
 ## Uploading your predictions
 
-We are currently preparing our website to accept your uploaded predictions. As soon as this is ready, you may upload your predictions. If you want to upload more than one set of predictions, generated by different methods, each set must be uploaded as a separate file. Please use the template provided, as the predictions will be parsed and analyzed with automated scripts, and if you violate the file format, you will receive an error message and your submission will not be accepted. A complete set of predictions constitutes predicted binding free energies for all required host-guest pairs, with predicted numerical uncertainties. We also encourage predictions of the binding enthalpies. Incomplete submissions - such as for a subset of compounds - will also be accepted, but will be treated as "verified" submissions rather than "ranked" submissions. However, omission of enthalpies and/or bonus cases will not cause a submission to be regarded as incomplete.
+[Submit your SAMPL7 predictions here](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/). Note our submission page resides on AWS at [http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/](http://sampl-submission.us-west-1.elasticbeanstalk.com/submit/), so don't be alarmed by the URL.
+
+If you want to upload more than one set of predictions, generated by different methods, each set must be uploaded as a separate file. Please use the template provided, as the predictions will be parsed and analyzed with automated scripts, and if you violate the file format, you will receive an error message and your submission will not be accepted. A complete set of predictions constitutes predicted binding free energies for all required host-guest pairs, with predicted numerical uncertainties. We also encourage predictions of the binding enthalpies. Incomplete submissions - such as for a subset of compounds - will also be accepted if desired (contact David Mobley if this is needed, as currently our submission system checks for completeness), but would be treated as "verified" submissions rather than "ranked" submissions. However, omission of enthalpies and/or bonus cases will not cause a submission to be regarded as incomplete.
 
 Names of the uploaded prediction files must begin with the name of the challenge component for which it contains predictions, as in the provided templates (i.e., GDCC, Clip, or CD, case-independently), and must end with an integer indicating which of your predictions for this host it contains. For example, if you want to submit one prediction file for the GDCC component, you might name it GDCC-myname-1.csv, where myname is arbitrary text of your choice. If you submit two prediction files for GDCC, you might name them GDCC-myname-1.txt and GDCC-myname-2.txt. Naming of guests, or host-guest combinations (as applicable) should be as illustrated in the submission templates.