User contributions for Btingle
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18 February 2021
- 18:0118:01, 18 February 2021 diff hist +10 Building The 3D Pipeline ZINC22 →SOFT_HOME
- 18:0018:00, 18 February 2021 diff hist +34 Building The 3D Pipeline ZINC22 →LONGCACHE
- 17:5817:58, 18 February 2021 diff hist +5 Building The 3D Pipeline ZINC22 →SOFT_HOME
- 17:5817:58, 18 February 2021 diff hist +26 Building The 3D Pipeline ZINC22 →SOFT_HOME
- 17:5817:58, 18 February 2021 diff hist +65 Building The 3D Pipeline ZINC22 →Script Arguments
9 February 2021
- 21:4021:40, 9 February 2021 diff hist −28 ZINC22:Singularity →how to build the singularity image current
- 21:3721:37, 9 February 2021 diff hist −7 ZINC22:Singularity →how to build the singularity image
- 21:3621:36, 9 February 2021 diff hist +170 ZINC22:Singularity →how to build the singularity image
- 21:3321:33, 9 February 2021 diff hist +396 ZINC22:Singularity →how to build the singularity image
8 February 2021
- 22:0222:02, 8 February 2021 diff hist +54 ZINC22:Singularity →how to use the singularity image
- 22:0122:01, 8 February 2021 diff hist +100 ZINC22:Singularity →how to build the singularity image
- 22:0022:00, 8 February 2021 diff hist +28 ZINC22:Singularity →how to build the singularity image
- 21:5921:59, 8 February 2021 diff hist +629 ZINC22:Singularity →how to build the singularity image
- 18:2218:22, 8 February 2021 diff hist −148 Building The 3D Pipeline ZINC22 →Running The Script
29 January 2021
- 03:2203:22, 29 January 2021 diff hist +553 How to dock in DOCK3.8 No edit summary
28 January 2021
- 21:3321:33, 28 January 2021 diff hist −21 How to dock in DOCK3.8 →Example: Running a lot of docking jobs
- 21:3221:32, 28 January 2021 diff hist −8 How to dock in DOCK3.8 →Example: Running a lot of docking jobs
- 21:2921:29, 28 January 2021 diff hist −61 How to dock in DOCK3.8 →Required Arguments
- 21:2821:28, 28 January 2021 diff hist 0 How to dock in DOCK3.8 →Optional Arguments
- 21:2721:27, 28 January 2021 diff hist +1,633 How to dock in DOCK3.8 No edit summary
- 21:1321:13, 28 January 2021 diff hist +39 How to dock in DOCK3.8 No edit summary
27 January 2021
- 19:1519:15, 27 January 2021 diff hist −1 Building The 3D Pipeline ZINC22 →Setup Instructions
- 18:5918:59, 27 January 2021 diff hist +11 Building The 3D Pipeline ZINC22 →LONGCACHE
- 18:5818:58, 27 January 2021 diff hist −295 Building The 3D Pipeline ZINC22 →Script Arguments
- 18:5618:56, 27 January 2021 diff hist +170 Building The 3D Pipeline ZINC22 →Running The Script
25 December 2020
- 07:4907:49, 25 December 2020 diff hist +73 2dload.py →Adding data with 2dload current
- 05:2905:29, 25 December 2020 diff hist +72 2dload.py →Adding data with 2dload
- 05:2405:24, 25 December 2020 diff hist +34 2dload.py →Adding data with 2dload
- 05:1905:19, 25 December 2020 diff hist +181 2dload.py No edit summary
- 05:1605:16, 25 December 2020 diff hist +14 2dload.py No edit summary
- 05:1505:15, 25 December 2020 diff hist +589 2dload.py →Adding data with 2dload
- 05:0305:03, 25 December 2020 diff hist +54 2dload.py →Adding data with 2dload
- 05:0005:00, 25 December 2020 diff hist +1,654 N 2dload.py Created page with "2dload.py is BKSLab's ZINC22 database management program, created by Benjamin Tingle. 2dload.py has three basic functionalities: * 2dload.py add * 2dload.py rollback * 2dloa..."
- 04:2704:27, 25 December 2020 diff hist +354 ZINC22 Partitions No edit summary current
- 00:4200:42, 25 December 2020 diff hist +450 ZINC22 Partitions No edit summary
- 00:3700:37, 25 December 2020 diff hist +168 ZINC22 Partitions No edit summary
- 00:3500:35, 25 December 2020 diff hist 0 File:Partitions new.PNG Btingle uploaded a new version of "File:Partitions new.PNG" current
- 00:3400:34, 25 December 2020 diff hist +16 ZINC22 Partitions No edit summary
- 00:3300:33, 25 December 2020 diff hist +77 ZINC22 Partitions No edit summary
- 00:3200:32, 25 December 2020 diff hist +1,804 N ZINC22 Partitions Created page with "The ZINC22 molecule database is sorted into buckets that we call tranches. The contents of each tranche are distinguished by a specific range of physiochemical properties, nam..."
24 November 2020
- 18:3318:33, 24 November 2020 diff hist +148 Building The 3D Pipeline ZINC22 No edit summary
20 November 2020
- 18:5918:59, 20 November 2020 diff hist +143 Restartable DOCK37 →Running & Restartability current
- 07:3407:34, 20 November 2020 diff hist 0 Restartable DOCK37 →Required Input
- 07:3007:30, 20 November 2020 diff hist +60 Restartable DOCK37 →Required Input
- 07:2807:28, 20 November 2020 diff hist +2 Restartable DOCK37 →Additional Notes
- 07:2607:26, 20 November 2020 diff hist +38 Restartable DOCK37 →Required Input
- 07:2507:25, 20 November 2020 diff hist +85 Restartable DOCK37 →Running & Restartability
- 05:2405:24, 20 November 2020 diff hist −6 Restartable DOCK37 →Running & Restartability
- 02:1002:10, 20 November 2020 diff hist +178 Restartable DOCK37 No edit summary
- 02:0402:04, 20 November 2020 diff hist +1 Restartable DOCK37 →Required Input
- 02:0402:04, 20 November 2020 diff hist +6 Restartable DOCK37 →Required Input
- 02:0202:02, 20 November 2020 diff hist +8 Restartable DOCK37 →Running & Restartability
- 02:0102:01, 20 November 2020 diff hist +2,449 N Restartable DOCK37 Created page with "==== Required Input ==== INDOCK split database index file The name of the split database index file is defined in INDOCK. Most INDOCK files name this file split_database_ind..."
18 November 2020
- 23:3223:32, 18 November 2020 diff hist +99 Building The 3D Pipeline ZINC22 →Running The Script
- 21:4321:43, 18 November 2020 diff hist +141 Building The 3D Pipeline ZINC22 →Repatriation
- 21:4121:41, 18 November 2020 diff hist +15 Building The 3D Pipeline ZINC22 →Running The Script
- 21:3921:39, 18 November 2020 diff hist +150 Building The 3D Pipeline ZINC22 →Setup Instructions
- 21:3721:37, 18 November 2020 diff hist +114 Building The 3D Pipeline ZINC22 →Setup Instructions
- 21:3121:31, 18 November 2020 diff hist −3 Building The 3D Pipeline ZINC22 →Setup Instructions
- 21:2721:27, 18 November 2020 diff hist +91 Building The 3D Pipeline ZINC22 →Running The Script
- 21:2521:25, 18 November 2020 diff hist −10 Building The 3D Pipeline ZINC22 →Running The Script
- 21:1921:19, 18 November 2020 diff hist −1 Building The 3D Pipeline ZINC22 →SBATCH_ARGS
- 21:1921:19, 18 November 2020 diff hist +127 Building The 3D Pipeline ZINC22 →Script Arguments
10 November 2020
- 20:1820:18, 10 November 2020 diff hist +125 Building The 3D Pipeline ZINC22 →Running The Script
- 20:1620:16, 10 November 2020 diff hist 0 Building The 3D Pipeline ZINC22 →Running The Script
9 November 2020
- 17:1817:18, 9 November 2020 diff hist +147 2dload →Command Description
5 November 2020
- 18:0718:07, 5 November 2020 diff hist −22 2dload →New 2D instructions
- 18:0618:06, 5 November 2020 diff hist +4,646 N 2dload Created page with "= New 2D instructions = === New commands === 1. pre_process_partition.bash [partition_id] [tranches] 2. python 2dload.py add [partition_id] [preprocess_file] [catalog_short..."
20 October 2020
- 18:2018:20, 20 October 2020 diff hist +22 Building The 3D Pipeline ZINC22 →Running The Script
- 18:1618:16, 20 October 2020 diff hist +289 Building The 3D Pipeline ZINC22 →Script Arguments
16 October 2020
- 01:3701:37, 16 October 2020 diff hist −30 Building The 3D Pipeline ZINC22 →Setup Instructions
- 01:2201:22, 16 October 2020 diff hist +9 Building The 3D Pipeline ZINC22 →Repatriation
- 01:1701:17, 16 October 2020 diff hist +221 Building The 3D Pipeline ZINC22 →Script Arguments
- 01:1401:14, 16 October 2020 diff hist +20 Building The 3D Pipeline ZINC22 →Running The Script
- 01:1301:13, 16 October 2020 diff hist +802 Building The 3D Pipeline ZINC22 →Input And Output
- 01:0301:03, 16 October 2020 diff hist +568 Building The 3D Pipeline ZINC22 No edit summary
- 00:5100:51, 16 October 2020 diff hist −59 Building The 3D Pipeline ZINC22 →Errors
- 00:4200:42, 16 October 2020 diff hist 0 Building The 3D Pipeline ZINC22 →Running The Script
- 00:4100:41, 16 October 2020 diff hist −1,283 Building The 3D Pipeline ZINC22 No edit summary
15 October 2020
- 22:3422:34, 15 October 2020 diff hist −3 Building The 3D Pipeline ZINC22 →Setup Instructions
- 22:3322:33, 15 October 2020 diff hist +1,308 Building The 3D Pipeline ZINC22 →Input And Output
- 22:3222:32, 15 October 2020 diff hist +16 Building The 3D Pipeline ZINC22 →Input And Output
- 22:3222:32, 15 October 2020 diff hist +186 Building The 3D Pipeline ZINC22 →Input And Output
- 22:3022:30, 15 October 2020 diff hist +78 Building The 3D Pipeline ZINC22 →Running The Script
- 22:2922:29, 15 October 2020 diff hist +24 Building The 3D Pipeline ZINC22 →Running The Script
- 22:2822:28, 15 October 2020 diff hist +59 Building The 3D Pipeline ZINC22 →Errors
- 22:2722:27, 15 October 2020 diff hist −1 Building The 3D Pipeline ZINC22 →Additional Notes
- 22:2522:25, 15 October 2020 diff hist +58 Building The 3D Pipeline ZINC22 →Setup Instructions
- 22:2422:24, 15 October 2020 diff hist +265 Building The 3D Pipeline ZINC22 →Running The Script
- 22:2222:22, 15 October 2020 diff hist +414 Building The 3D Pipeline ZINC22 →Running The Script
- 20:1720:17, 15 October 2020 diff hist +224 Building The 3D Pipeline ZINC22 →Running The Script
18 September 2020
- 20:2120:21, 18 September 2020 diff hist +12 Building The 3D Pipeline ZINC22 →Setup Instructions
- 20:0920:09, 18 September 2020 diff hist +4,201 N Building The 3D Pipeline ZINC22 Created page with "== Introduction == The 3D pipeline is a collection of scripts and software packages that enable the massively parallel creation of dockable 3D molecules. == Requirements == ..."
16 July 2020
- 22:4622:46, 16 July 2020 diff hist +48 New 3D Building On Wynton →Revised 3D Building On Wynton current
- 22:4422:44, 16 July 2020 diff hist +3 New 3D Building On Wynton →Revised 3D Building On Wynton
- 22:2322:23, 16 July 2020 diff hist +580 New 3D Building On Wynton No edit summary
- 03:2703:27, 16 July 2020 diff hist +1,798 N New 3D Building On Wynton Created page with " <nowiki> have re-vamped the script for the 2nd time, this time configured to use SGE on Wynton. the script is based in ~/zinc-3d-build-3 on jji@wynton I've had to re-install/..."
30 June 2020
- 18:2718:27, 30 June 2020 diff hist +12 ZINC-22:3D Building →Introduction
- 18:2518:25, 30 June 2020 diff hist +18 ZINC-22:3D Building →Usage
- 18:2418:24, 30 June 2020 diff hist +19 ZINC-22:3D Building →Example Usage
- 18:2418:24, 30 June 2020 diff hist +8 ZINC-22:3D Building →Usage
- 18:2318:23, 30 June 2020 diff hist +119 ZINC-22:3D Building →Usage
- 18:2218:22, 30 June 2020 diff hist −7 ZINC-22:3D Building →Usage
- 18:2118:21, 30 June 2020 diff hist +1,358 N ZINC-22:3D Building Created page with "= Introduction = You can request access to the zinc 3d build repository here: https://github.com/btingle/zinc-3d-build The contents of this github can be found on /nfs/home..."
22 June 2020
- 22:5922:59, 22 June 2020 diff hist +4 How To Load New ZINC Databases →Email to Abhinav and Khanh, 6/22
- 22:5922:59, 22 June 2020 diff hist +42 How To Load New ZINC Databases →Email to Abhinav and Khanh, 6/22
- 22:5722:57, 22 June 2020 diff hist +2,329 How To Load New ZINC Databases →Email to Khanh, 6/15
15 June 2020
- 18:4618:46, 15 June 2020 diff hist +8 How To Load New ZINC Databases →Email to Khanh, 6/15
- 18:4518:45, 15 June 2020 diff hist −24 How To Load New ZINC Databases →Email to Khanh, 6/15
- 18:4418:44, 15 June 2020 diff hist +216 How To Load New ZINC Databases →Email to Khanh, 6/15
- 18:0918:09, 15 June 2020 diff hist +1,484 How To Load New ZINC Databases →Logging
11 June 2020
- 22:0222:02, 11 June 2020 diff hist +9 How To Load New ZINC Databases →ZINC_PORT
- 21:5521:55, 11 June 2020 diff hist +32 How To Load New ZINC Databases →Start
- 20:4120:41, 11 June 2020 diff hist +53 How To Load New ZINC Databases →Running the Script
- 20:4020:40, 11 June 2020 diff hist +2 How To Load New ZINC Databases →Running the Script
- 20:3820:38, 11 June 2020 diff hist +2,737 N How To Load New ZINC Databases Created page with "== Start == * log in to machine * check that /local2/load directory exists and is owned by xyz * do "netstat -plunt" and check ports 5434-54XX to see which tin databases are o..."
31 May 2020
- 00:0800:08, 31 May 2020 diff hist −1 Why Loading ZINC Is So Slow →a. sorting & queries current
- 00:0500:05, 31 May 2020 diff hist +22 Why Loading ZINC Is So Slow →other
- 00:0000:00, 31 May 2020 diff hist +506 Why Loading ZINC Is So Slow →c. improvement
30 May 2020
- 18:0918:09, 30 May 2020 diff hist −4 Why Loading ZINC Is So Slow →c. improvement
- 18:0818:08, 30 May 2020 diff hist +22 Why Loading ZINC Is So Slow →c. improvement
- 18:0718:07, 30 May 2020 diff hist +36 Why Loading ZINC Is So Slow →c. improvement
- 18:0618:06, 30 May 2020 diff hist +243 Why Loading ZINC Is So Slow →b. indexes
- 18:0118:01, 30 May 2020 diff hist +12 Why Loading ZINC Is So Slow No edit summary
- 18:0118:01, 30 May 2020 diff hist +10 Why Loading ZINC Is So Slow No edit summary
- 18:0018:00, 30 May 2020 diff hist +1,615 N Why Loading ZINC Is So Slow Created page with "/nfs/home/xyz/btingle/zinc_deploy/zincload-catalog.sh the problem is with the "resolution" and "loading" steps of the catalog script. these steps ensure the uniqueness of mol..."
29 May 2020
- 04:0704:07, 29 May 2020 diff hist +8 Loading And Creating ZINC Partitions Automatically →TODO current
28 May 2020
- 05:4605:46, 28 May 2020 diff hist +1 Loading And Creating ZINC Partitions Automatically →TODO
- 05:3305:33, 28 May 2020 diff hist +94 Loading And Creating ZINC Partitions Automatically →1. Running the script
- 04:2604:26, 28 May 2020 diff hist −10 Loading And Creating ZINC Partitions Automatically →Generating a Partition Configuration
- 03:1703:17, 28 May 2020 diff hist −1 Loading And Creating ZINC Partitions Automatically →2. Generating the partitions
- 03:1603:16, 28 May 2020 diff hist 0 N File:Partitions new.PNG No edit summary
- 03:1603:16, 28 May 2020 diff hist +3,049 N Loading And Creating ZINC Partitions Automatically Created page with "In this wiki page I will describe the journey of 1) generating a partition configuration for a set of fine-tranched molecules 2) deploying an individual partition database..."
22 April 2020
- 20:0320:03, 22 April 2020 diff hist +273 Zfs →Tue Apr 21 2020
- 19:5919:59, 22 April 2020 diff hist +619 Zfs →Tue Apr 21 2020
21 April 2020
- 22:1422:14, 21 April 2020 diff hist +23 Zfs →Mon Apr 20 2020
- 22:1222:12, 21 April 2020 diff hist +315 Zfs →Mon Apr 20 2020
17 April 2020
- 23:2323:23, 17 April 2020 diff hist +84 Performing a Query on 22B Molecules →Logging in to the Round Table Manager current
- 23:2223:22, 17 April 2020 diff hist −112 Performing a Query on 22B Molecules →Logging in to the Round Table Manager
- 23:2123:21, 17 April 2020 diff hist −997 Performing a Query on 22B Molecules No edit summary
- 23:1823:18, 17 April 2020 diff hist 0 N File:Manager-2-upload.PNG No edit summary current
- 23:1823:18, 17 April 2020 diff hist 0 N File:Manager-2-query.PNG No edit summary current
- 23:1823:18, 17 April 2020 diff hist 0 N File:Manager-2.PNG No edit summary current
- 02:0502:05, 17 April 2020 diff hist +21 Category:Arthor No edit summary current
- 02:0402:04, 17 April 2020 diff hist +1,718 N Category:Arthor Created page with " Arthor High-Performance Chemical Database Searching NextMove Software's Arthor technology (named after Merlin's apprentice) pushes the performance limits of chemical databa..."
- 02:0302:03, 17 April 2020 diff hist +20 Querying All Arthor Databases With Python No edit summary current
- 02:0002:00, 17 April 2020 diff hist +1,260 N Querying All Arthor Databases With Python Created page with "Excerpt from email: Alternatively, I have a python script that will perform a SMARTS query on all compatible arthor databases. This script is located on the lab NFS at: /mnt/..."
16 April 2020
- 20:5720:57, 16 April 2020 diff hist 0 Performing a Query on 22B Molecules →Performing a query on multiple databases
- 20:5720:57, 16 April 2020 diff hist 0 Performing a Query on 22B Molecules →Performing a query on multiple databases
- 20:5620:56, 16 April 2020 diff hist 0 Performing a Query on 22B Molecules →Performing a query on multiple databases
- 20:5620:56, 16 April 2020 diff hist +27 Performing a Query on 22B Molecules →Performing a query on multiple databases
- 20:5520:55, 16 April 2020 diff hist 0 N File:Query example.PNG No edit summary current
15 April 2020
- 22:4022:40, 15 April 2020 diff hist +1 Performing a Query on 22B Molecules →Introduction
- 22:2222:22, 15 April 2020 diff hist +117 Performing a Query on 22B Molecules →Other Endpoints
- 22:1922:19, 15 April 2020 diff hist +157 Performing a Query on 22B Molecules →Other Endpoints
- 22:1822:18, 15 April 2020 diff hist +1 Performing a Query on 22B Molecules →Other Endpoints
- 22:1722:17, 15 April 2020 diff hist +31 Performing a Query on 22B Molecules →Logging in to the Round Table Manager
- 22:1622:16, 15 April 2020 diff hist 0 N File:Managerscreencap.PNG No edit summary current
- 22:1522:15, 15 April 2020 diff hist +82 m Performing a Query on 22B Molecules →Uploading a new Database
- 22:1322:13, 15 April 2020 diff hist +3,021 N Performing a Query on 22B Molecules Created page with "== Introduction == Say you are a scientist, and you need to find all the molecules you can that match a specific query. To start, you could go to the arthor round table server..."
28 March 2020
- 21:3721:37, 28 March 2020 diff hist +3 Setting Up An Automatic SSH Tunnel To Epsilon No edit summary current
- 21:3121:31, 28 March 2020 diff hist +24 m Setting Up An Automatic SSH Tunnel To Epsilon Added category tag
- 21:2221:22, 28 March 2020 diff hist +371 m Setting Up An Automatic SSH Tunnel To Epsilon →Setting up your Bitvise profile for Epsilon
- 21:1621:16, 28 March 2020 diff hist +8 Setting Up An Automatic SSH Tunnel To Epsilon →Setting up your Bitvise profile for Epsilon
- 21:1521:15, 28 March 2020 diff hist +124 Setting Up An Automatic SSH Tunnel To Epsilon →Setting up your Bitvise profile for Epsilon
- 21:1321:13, 28 March 2020 diff hist +22 N File:Bitvisesocks.PNG bitvise socks settings current
- 21:1321:13, 28 March 2020 diff hist +22 N File:Bitviselogin.PNG bitvise login settings current
- 21:1221:12, 28 March 2020 diff hist +25 N File:Bitvisehost.PNG bitvise host key settings current
- 21:1221:12, 28 March 2020 diff hist +27 N File:Bitviseclient.PNG bitvise client key settings current
- 21:1121:11, 28 March 2020 diff hist 0 N File:Bitvisec2s.PNG No edit summary current
- 21:1121:11, 28 March 2020 diff hist +3,855 N Setting Up An Automatic SSH Tunnel To Epsilon Created page with "With the Coronavirus not showing any signs of letting up, we need to be prepared to work on projects remotely for some time. When working on projects remotely, Lab members mus..."
