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• 00:13, 14 June 2023 Btingle talk contribs created page All About DB2 Files (Created page with "== The brass tacks == DB2 files encode & compress 3D molecule rotomers, sometimes referred to as conformations. DB2 files do not store the dihedral angles of rotomers, but instead the per-atom coordinates resulting from those angles Atoms of different rotomers whose coordinates overlap are merged together in db2 files (how this is done will be detailed more later), thus allowing DOCK to avoid double-calculating per-atom energies == The nitty gritty == DB2 is a text fo...")
• 22:21, 31 May 2023 Btingle talk contribs created page Installing The 3D Pipeline ZINC22 (Created page with "Installation of the 3D pipeline is somewhat tricky- the environment is very particular about which versions of which software should be used. It is thus easiest to copy the exact software packages we use from our servers- this should work provided they are installed in a 64-bit linux architecture, though depending on the distribution certain shared libraries may be missing. == Setting up the installation root == First find a suitable directory which will serve as the r...")
• 20:29, 2 March 2023 Btingle talk contribs created page Repackaging DB2 DOCK38 (Created page with "The following is a script for repackaging 3D pipeline results. First, here is the script: <nowiki> #!/bin/bash # make_tarballs.bash # required parameter RESULT_DIRECTORY=$1 # optional parameters WORKING_DIRECTORY=${WORKING_DIRECTORY-/tmp/$(whoami)} PACKAGES_PER_PACKAGE=${PACKAGES_PER_PACKAGE-100} PACKAGE_TYPE=${PACKAGE_TYPE-db2.gz} PACKAGE_TYPE_SHORT=$(echo $PACKAGE_TYPE | cut -d'.' -f1) echo WORKING_DIRECTORY=$WORKING_DIRECTORY mkdir -p $WORKING_DIRECTORY && cd $WO...")
• 02:14, 1 December 2022 Btingle talk contribs created page SUBDOCK DOCK3.8 (Created page with "== how to use subdock == Subdock is a utility for running UCSF docking workloads across multiple platforms. There are four essential ingredients that go in to every docking...")
• 20:38, 19 October 2022 Btingle talk contribs created page File:Step1-docktut-again.png
• 20:38, 19 October 2022 Btingle talk contribs uploaded File:Step1-docktut-again.png
• 20:33, 19 October 2022 Btingle talk contribs uploaded File:Stepwhatever2.png
• 20:33, 19 October 2022 Btingle talk contribs created page File:Stepwhatever2.png
• 20:33, 19 October 2022 Btingle talk contribs created page File:Stepwhatever.png
• 20:33, 19 October 2022 Btingle talk contribs uploaded File:Stepwhatever.png
• 20:25, 19 October 2022 Btingle talk contribs created page File:Step6.png
• 20:25, 19 October 2022 Btingle talk contribs uploaded File:Step6.png
• 20:21, 19 October 2022 Btingle talk contribs created page File:Awsdock-Step3-flowchart.png
• 20:21, 19 October 2022 Btingle talk contribs uploaded File:Awsdock-Step3-flowchart.png
• 20:15, 19 October 2022 Btingle talk contribs created page File:Step3.png
• 20:15, 19 October 2022 Btingle talk contribs uploaded File:Step3.png
• 20:12, 19 October 2022 Btingle talk contribs created page File:Awsdock-imagetut-step1.png
• 20:12, 19 October 2022 Btingle talk contribs uploaded File:Awsdock-imagetut-step1.png
• 20:48, 3 August 2022 Btingle talk contribs created page Using AWS Setup For Cloud Computation (Created page with "= Introduction to the AWS Setup platform = The concept of "the cloud" as a platform for computation is somewhat mystified. Scientists talk about running their calculations "i...")
• 06:06, 27 July 2022 Btingle talk contribs created page AWS DOCK Environment Setup Advanced Usage (Created page with "= Advanced Usage/Configuration Usage = If you followed the tutorial above, you may have noticed that the create-aws-batch-env.bash script was provided a file, awsdock.config,...")
• 16:57, 26 July 2022 Btingle talk contribs created page File:Spotlimits.png
• 16:57, 26 July 2022 Btingle talk contribs uploaded File:Spotlimits.png
• 16:59, 25 July 2022 Btingle talk contribs created page DOCK memory and CPU benchmark (Created page with "Excerpt from email between Ben Tingle and Jiankun Lyu: <nowiki> JK- I have some more info on how threads/cpus work. It seems that utilizing threads does give more power, but...")
• 03:30, 22 June 2022 Btingle talk contribs created page Category:AWS DOCK (Created page with "Protocols for running DOCK software on AWS. Specifically DOCK 3.8 (and others in the DOCK3 family) Despite these protocols being tailored for the DOCK3 family of software, th...")
• 00:15, 22 June 2022 Btingle talk contribs created page File:S3pricing.png
• 00:15, 22 June 2022 Btingle talk contribs uploaded File:S3pricing.png
• 23:53, 21 June 2022 Btingle talk contribs created page Docking Submission On AWS (Created page with "=== Prerequisites === * You've followed the tutorial for setting up the environment: AWS DOCK Environment Setup * Following from the previous requirement, you have the a...")
• 23:07, 21 June 2022 Btingle talk contribs uploaded File:Aws docking env.png
• 23:07, 21 June 2022 Btingle talk contribs created page File:Aws docking env.png
• 00:19, 18 June 2022 Btingle talk contribs created page File:Terminateinstance.png
• 00:19, 18 June 2022 Btingle talk contribs uploaded File:Terminateinstance.png
• 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched3.png
• 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched3.png
• 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched2.png
• 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched2.png
• 00:16, 18 June 2022 Btingle talk contribs uploaded File:Instancelaunched1.png
• 00:16, 18 June 2022 Btingle talk contribs created page File:Instancelaunched1.png
• 00:15, 18 June 2022 Btingle talk contribs uploaded File:Configstorage.png
• 00:15, 18 June 2022 Btingle talk contribs created page File:Configstorage.png
• 00:15, 18 June 2022 Btingle talk contribs created page File:Keypair.png
• 00:15, 18 June 2022 Btingle talk contribs uploaded File:Keypair.png
• 00:13, 18 June 2022 Btingle talk contribs uploaded File:Instancetype.png
• 00:13, 18 June 2022 Btingle talk contribs created page File:Instancetype.png
• 00:13, 18 June 2022 Btingle talk contribs uploaded File:Launchinstances.png
• 00:13, 18 June 2022 Btingle talk contribs created page File:Launchinstances.png
• 23:42, 17 June 2022 Btingle talk contribs created page Docking Analysis On AWS (Created page with "=== Prerequisites === github personal access token & DOCK repository access rights (https://docs.github.com/en/authentication/keeping-your-account-and-data-secure/creating-a-...")
• 23:16, 13 June 2022 Btingle talk contribs created page OCI Slurm Autoscaling (Created page with "* Create a compartment for your autoscaling resources <nowiki> SlurmAutoScaling</nowiki> * Create a dynamic group for autoscaling instances. Add the following as a matching...")
• 21:48, 8 June 2022 Btingle talk contribs created page Search zinc22.py (Created page with " <nowiki> usage: search_zinc22.py [-h] [--configuration-server-url CONFIGURATION_SERVER_URL] zinc_id_in results_out positional...")
• 21:40, 19 May 2022 Btingle talk contribs created page Legacy IDs in ZINC22 (Created page with "ZINC22 is by far the largest chemical database this lab has built, and with it's fantastic size we have found fantastic new difficulties. When we receive chemical libraries f...")
• 04:27, 20 January 2022 Btingle talk contribs created page AWS DOCK Environment Setup (Created page with "This page pertains to the scripts created by Benjamin Tingle to set up an environment for running DOCK workloads in AWS. WIP: Not complete, just saving progress = Getting S...")