All public logs

Combined display of all available logs of DISI. You can narrow down the view by selecting a log type, the username (case-sensitive), or the affected page (also case-sensitive).

• 00:09, 7 October 2025 Khtang talk contribs created page Connect VSCode to cluster (Created page with "== Link == https://code.visualstudio.com/docs/remote/ssh == Instruction == === 1. Install extension === Go to 'Extension' tab in VSCode, look up 'Remote-SSH' and install === 2. Setup tunnel === To connect with VS code, forward the 22 port on the machine that you’d like to use using the following command ssh -CL localhost:2222:epyc:22 <username>@portal3.ucsf.bkslab.org === 3. Setup configuration in Remote - SSH === - Click on the 'Connect to...' under Start in the 'Welc...")
• 18:40, 11 September 2025 Khtang talk contribs created page Looking up CAS (Created page with "CAS registry number is the unique identification number assigned by Chemical Abstract Service for every chemical substance identified in open scientific literature. Looking them up could be a tedious task. There are several CAS lookup APIs services: PUBMED : https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/name/[CAS]/property/CanonicalSMILES/JSON CAS.org : https://commonchemistry.cas.org/api/detail?cas_rn=[CAS]")
• 18:25, 28 August 2025 User account Pseemann talk contribs was created by Khtang talk contribs and password was sent by email
• 18:25, 28 August 2025 Khtang talk contribs created page User:Pseemann (Creating user page for new user.)
• 18:25, 28 August 2025 Khtang talk contribs created page User talk:Pseemann (Welcome!)
• 22:40, 24 July 2025 User account Kholland talk contribs was created by Khtang talk contribs and password was sent by email
• 22:40, 24 July 2025 Khtang talk contribs created page User:Kholland (Creating user page for new user.)
• 22:40, 24 July 2025 Khtang talk contribs created page User talk:Kholland (Welcome!)
• 21:15, 21 March 2025 Khtang talk contribs changed group membership for Sstrizhov from (none) to administrator
• 20:17, 24 January 2025 Khtang talk contribs created page CHARMM (Created page with "CHARMM is a molecular simulation software from Harvard. = Install CHARMM = == Requirements == gcc --version * Upgrade to at least GCC 7 ( if need) https://linuxhostsupport.com/blog/how-to-install-gcc-on-centos-7/ * Upgrade Cmake (version 3+) Please make sure that you are using the same C and Fortran compiler version for these dependencies below otherwise CHARMM won’t compile wget https://cmake.org/files/v3.20/cmake-3.20.5.tar.gz tar xvzf cmake-3.20.5.tar.gz cd...")
• 07:51, 14 January 2025 Khtang talk contribs moved page Add Tools18 module to Add TLDR module without leaving a redirect
• 19:48, 7 January 2025 User account Sstrizhov talk contribs was created by Khtang talk contribs and password was sent by email (serge's account)
• 19:48, 7 January 2025 Khtang talk contribs created page User:Sstrizhov (Creating user page for new user.)
• 19:48, 7 January 2025 Khtang talk contribs created page User talk:Sstrizhov (Welcome!)
• 21:53, 18 March 2024 Khtang talk contribs created page Renew Schrodinger Licenses (Created page with "'''<big>Cluster 0 and 2 licenses are expired on March 15th annually. </br> Contact licensing@schrodinger.com (CC John and Brian) and tell them that you are from Shoichet Lab and would like to renew TWO licenses. They will send the Cluster 0 license to John and Cluster 2 license to Brian</big>''' === Get License File === Get the email about Schrodinger license keys ready for retrieval from John or Brian.</br> Click the link that said '''please user this form to generate...")
• 00:05, 22 February 2024 Khtang talk contribs deleted page Notes from first attempt at globus (content was: "https://www.globus.org/globus-connect-server In an attempt to install Globus Connect Server, here is my notes of what I have done so far. Note: I have tried installed Globus on gimel2, tau. So far no luck getting it working Detail complete guide https://docs.globus.org/globus-connect-server-installation-guide/ https://www.h3abionet.org/images/Technical_guides/L2_04_How_To_Setup_and_Configure_Globus_Connect_Endpoint_V1.5.pdf === Open required TCP Ports === ==== Check if FQ...")
• 22:20, 15 February 2024 Khtang talk contribs moved page Schrodinger notes to Schrodinger
• 21:11, 13 February 2024 Khtang talk contribs created page MediaWiki:Sidebar (Created page with " * navigation ** [https://calendar.google.com/calendar/u/6/embed?src=90hc5i060oggekk2s3c8sluf4g@group.calendar.google.com&pvttk=b015223b9cc576dce92e6cc7698935cd&csspa=1 BKS Calendar] ** mainpage|mainpage-description ** recentchanges-url|recentchanges ** randompage-url|randompage ** helppage|help-mediawiki * SEARCH * TOOLBOX * LANGUAGES")
• 21:08, 13 February 2024 Khtang talk contribs changed group membership for Bks.labmanager from (none) to interface administrator
• 20:44, 13 February 2024 Khtang talk contribs blocked 小千代我老婆 talk contribs with an expiration time of indefinite (account creation disabled)
• 19:45, 22 November 2023 User account Bks.labmanager talk contribs was created by Khtang talk contribs and password was sent by email
• 19:45, 22 November 2023 Khtang talk contribs created page User:Bks.labmanager (Creating user page for new user.)
• 19:45, 22 November 2023 Khtang talk contribs created page User talk:Bks.labmanager (Welcome!)
• 20:57, 20 September 2023 Khtang talk contribs created page Chemistry commons Notes (Created page with "== Database Management == Source chemistry commons source /nfs/soft/anaconda3/bin/activate ~khtang/.conda/envs/chemcommons === Import data from Spreadsheet === ** This will be deprecated once we switched to use postgres bash /nfs/home/khtang/work/gitlab/ChemistryCommons-2-0/CC_load_scripts/load_common.bash import mem2 [Reactions_Reference_Spreadsheet.xlsx] === Export Chemistry Commons DB === Run this script to create a snapshot of the database and JSON files for Enum...")
• 22:32, 13 March 2023 Khtang talk contribs created page LUNA (Created page with "'''LUNA''' is drug discovery Python toolkit developed by Keiser Lab at UCSF Github repo https://github.com/keiserlab/LUNA == Install Instruction == If you have trouble following LUNA's conda environment setup instruction, try this conda create -n luna-env -c schrodinger pymol -y conda activate luna-env conda install -c conda-forge rdkit seaborn openbabel pip xopen colorlog networkx -y pip install mmh3==2.5.1 pip install biopython==1.72 BKS Cluster has LUNA conda...")
• 06:18, 4 November 2022 Khtang talk contribs created page Slurm Installation Guide (Created page with "This page will show you how to setup and configure a Slurm queueing system. Useful link: https://wiki.fysik.dtu.dk/Niflheim_system/Slurm_installation/ == Pre-installation ==...")
• 22:39, 1 September 2022 User account Omailhot talk contribs was created by Khtang talk contribs and password was sent by email
• 22:39, 1 September 2022 Khtang talk contribs created page User:Omailhot (Creating user page for new user.)
• 22:39, 1 September 2022 Khtang talk contribs created page User talk:Omailhot (Welcome!)
• 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Swbatch to TLDR:swbatch without leaving a redirect
• 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Strain to TLDR:strain without leaving a redirect
• 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Newbuild3d to TLDR:newbuild3d without leaving a redirect
• 05:29, 9 August 2022 Khtang talk contribs moved page TLDR:Extrema to TLDR:extrema without leaving a redirect
• 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:DUDE-Z to TLDR:dude-z without leaving a redirect
• 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:Bootstrap2 to TLDR:bootstrap2
• 05:28, 9 August 2022 Khtang talk contribs moved page TLDR:Bootstrap1 to TLDR:bootstrap1 without leaving a redirect
• 05:27, 9 August 2022 Khtang talk contribs moved page TLDR:Bioisostere to TLDR:bioisostere without leaving a redirect
• 05:26, 9 August 2022 Khtang talk contribs moved page TLDR:Arthorbatch to TLDR:arthorbatch without leaving a redirect
• 06:15, 8 August 2022 Khtang talk contribs created page TLDR:Swbatch (Created page with "== Purpose == Running multiple queries on SmallWorld. See https://sw.docking.org/search.html == Inputs == * molecules.ism == Outputs == TBD == Notes == TBD")
• 06:12, 8 August 2022 Khtang talk contribs created page TLDR:Newbuild3d (Created page with "== Purpose == Prepare a 3D library for docking with '''DOCK3.8''' pipeline in several formats used by popular docking programs: sdf, db2, mol2, pdbqt, solv == Inputs == * mol...")
• 05:37, 8 August 2022 Khtang talk contribs created page TLDR:Extrema (Created page with "== Purpose == Generate an equivalent number of charged (-2, -1, 0, +1, +2) molecules in the molecular weight and cLogP property space of your input SMILES molecules. These cha...")
• 05:32, 8 August 2022 Khtang talk contribs created page TLDR:Bootstrap2 (Created page with "== Purpose == Get 95% confidence interval from bootstrapping. == Inputs == * decoys.name * ligands.name * ranked_list_1 * ranked_list_2 == Outputs == TBD == Notes == TBD")
• 05:30, 8 August 2022 Khtang talk contribs created page TLDR:Bootstrap1 (Created page with "== Purpose == Compare performance of 2 docking methods with p value == Inputs == * decoys.name * ligands.name * ranked_list_1 * ranked_list_2 == Outputs == TBD == Notes == TBD")
• 05:20, 8 August 2022 Khtang talk contribs created page TLDR:Strain (Created page with "== Purpose == This strain filter software is a fast and reliable approach to calculate the strain energy of millions of small molecules. == Inputs == * mol2 file contains mole...")
• 04:55, 8 August 2022 Khtang talk contribs created page TLDR:DUDE-Z (Created page with "== Purpose == Assemble decoys for docking using the DUDEZ approach. See https://dudez.docking.org for sample data == Inputs == * Ligands provided in smiles format (actives.sm...")
• 04:45, 8 August 2022 Khtang talk contribs created page TLDR:Bioisostere (Created page with "== Purpose == To find analogs of your active compounds that you can use to explore SAR by catalogs around your hits. == Inputs == * a starting molecule in txt file (one at a...")
• 17:53, 5 August 2022 User account Jocastanon talk contribs was created by Khtang talk contribs and password was sent by email
• 17:53, 5 August 2022 Khtang talk contribs created page User:Jocastanon (Creating user page for new user.)
• 17:53, 5 August 2022 Khtang talk contribs created page User talk:Jocastanon (Welcome!)
• 21:54, 4 August 2022 Khtang talk contribs created page Dimorphite-DL (Created page with "'''Dimorphite-DL is an open-source software for enumerating ionization states of molecules created by [https://durrantlab.pitt.edu/ Durrant Lab] at University of Pittsburgh.''...")