SOC workstation - Revision history

Wtitulaer at 13:00, 30 January 2025

2025-01-30T13:00:08Z

← Older revision		Revision as of 13:00, 30 January 2025
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	\|+ Software installed on the SOC workstation (last updated 30.01.2025)		\|+ Software installed on the SOC workstation (last updated 30.01.2025)
	! Software !! Intended purpose !! License		! Software !! Intended purpose !! License
			\|-
			\| 7-zip \|\| Compressing and decompressing .zip files \|\| n.a.
			\|-
			\| Avogardo \|\| Small molecule modelling \|\| n.a.
			\|-
			\| ChemOffice \|\| Drawing molecules (chemdraw) or saving as .sdf \|\| RU
	\|-		\|-
	\| GOLD\|\| Precise molecular docking with a genetic algorithm (GA) for pose sampling\|\| Academic, RU-broad from solid state chemistry		\| GOLD\|\| Precise molecular docking with a genetic algorithm (GA) for pose sampling\|\| Academic, RU-broad from solid state chemistry
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	\|-		\|-
	\| MOE\|\| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. \|\| Rutjes group exclusive, 1 license		\| MOE\|\| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. \|\| Rutjes group exclusive, 1 license
			\|-
			\| Wincoot \|\| Inspecting electron density maps (EDMs) of biomolecules WARNING! Downloading precomputed EDM .mtz files from the PDB is no longer possible \|\| Academic
	\|- style="color: red"		\|- style="color: red"
	\| YASARA Structure (currently no license) \|\| Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program \|\| Academic, wtitulaer personal		\| YASARA Structure (currently no license) \|\| Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program \|\| Academic, wtitulaer personal

Wtitulaer at 12:56, 30 January 2025

2025-01-30T12:56:41Z

← Older revision		Revision as of 12:56, 30 January 2025
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	\|-		\|-
	\| MOE\|\| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. \|\| Rutjes group exclusive, 1 license		\| MOE\|\| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. \|\| Rutjes group exclusive, 1 license
	\|-		\|- style="color: red"
	\| style="color:red" YASARA Structure (no		\| YASARA Structure (currently no license) \|\| Homology Modelling, Protein-ligand modelling, molecular dynamics (MD), Visualization program \|\| Academic, wtitulaer personal
	\|}		\|}

Wtitulaer at 12:53, 30 January 2025

2025-01-30T12:53:32Z

← Older revision		Revision as of 12:53, 30 January 2025
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	! Software !! Intended purpose !! License		! Software !! Intended purpose !! License
	\|-		\|-
	\| ~~test~~ \|\| ~~test~~ \|\| ~~test~~		\| GOLD\|\| Precise molecular docking with a genetic algorithm (GA) for pose sampling\|\| Academic, RU-broad from solid state chemistry
			\|-
			\| Mogul\|\| Torsion angle checking against the CSD \|\| Academic, RU-broad from solid state chemistry
			\|-
			\| Conquest\|\| Software to search the CSD\|\| Academic, RU-broad from solid state chemistry
			\|-
			\| MOE\|\| Primary use of the workstation, all-round software for LBDD and SBDD such as: QSAR, Pharmacophores, homology modelling, (template-based) docking, protein-ligand modelling, fragment-growing, library enumeration, visualization. \|\| Rutjes group exclusive, 1 license
			\|-
			\| style="color:red" YASARA Structure (no
	\|}		\|}

Wtitulaer at 12:48, 30 January 2025

2025-01-30T12:48:09Z

@@ Line 3: / Line 3: @@
 '''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl
-=Maintenance=
+==Available software==
 Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.

Wtitulaer at 17:14, 29 January 2025

2025-01-29T17:14:45Z

← Older revision		Revision as of 17:14, 29 January 2025
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	'''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl		'''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl

	~~{{{Access to the Station}}}~~
	~~{{{To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}}~~

	=Maintenance=		=Maintenance=
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	The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.		The idea is that all software updates / maintenance can be performed from the admin account unless stated differently on this page.
	Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.		Here follows a list of common practices per software that the PC runs that should be checked from time-to-time.
			==Hardware checks==
			===Disk checks (2/year)===
			Disk checks should be performed twice per year for each disk (raid 1 mirror setup). This can be done by using the desktop folder maintenance and running the listed commands in a Windows cmd administrator shell.
			Check the 'SMART overall-health self-assessment test result:' it should say PASSED and if not Hakim should be contacted with the info also found after running this command.
			Similarly, the Intel rapid storage app (accessible through the popup icon in the footer) should have green indications that everything is working as it should.

	==~~Disk checks (2/year)~~==		===CCleaner===
			Should run automatically but if changes needed, these need to be reconfigured per user.

			===Windows updates (2/year)===
			Run windows 10 updates twice per year and book a slot for this.

	==~~Teamviewer~~==		==Software updating==
	~~Privacy black screen.~~		The idea is to conservatively update the system. Should updates still be needed, here are recommendations.
	~~Managed from admin account.~~
	~~At advanced settings you can fix Disable local input and Enable Blackscreen. Also have full access, deactivate random password.~~
	~~Personal password~~ is ~~the other password that allows~~ to ~~connect without~~ the ~~need to fill it in~~.
	~~Safe way~~, ~~make screenshots before updating~~.

	~~Licentiebeheer ILS Wietske (RU), Samuel handels the payment.~~		===Teamviewer===
	===~~New user~~===		Teamviewer is managed from the admin account with the gear icon (requiring the Settings password).
	~~- Make a new user yourself~~ with a password		When update is needed, ensure to make screenshots of all settings prior to updating. The most important settings to keep:
	~~- Remove everything at Advanced apart from log sessions~~		* At advanced settings, Disable local input and Enable blackscreen
	~~- Permission~~: ~~user~~		* Ensure Full Access is selected
	~~- User receives email~~ and ~~makes account~~		* Deactivate random password
	~~- Now the user~~ is ~~active and~~ the ~~share can be assigned~~ to ~~the user with~~ a ~~Read-only permission~~		* Personal password is the Access password for SOCMOE that allows users to enter a remote session without needing to fill in another password.

	~~Incoming LAN connections: accept~~ (~~needed~~ to ~~have it run from ru-network as well)~~.		==Transfer of access==
			Important is that 'Licentiebeheer ILS' knows who is in charge of the station. Our current contact is Wietske (RU) who emails on if license for Teamviewer needs to be continued after which Samuel handels the payment.

			=Guidelines for adding new users=
			==Terms of use==
			Users who apply for the use of the machine must all accept it terms of conditions (the standard email with the same file). @Willem, could include which software can be used by whom.

			==New user Teamviewer (remote access)==
			Using the online [login.teamviewer.com TeamViewer] with your own user login (requires being added as an admin previously).
			Then do the following:
			* Admin makes a new user with the specified email address (preferably RU or science) with a password
			* Admin removes everything at the Advanced settings apart from the 'log sessions' setting
			* Admin sets permission to user
			* User receives email and makes the account
			* Now that the user is actually active, the share can be assigned to the user with a Read-only permission.

			Furthermore, it is important here the setting 'Incoming LAN connections' is set to 'accept' since otherwise people on the RU-network will not be able to connect remotely.

	==Booking==		==Booking==
	Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.		Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.

	~~==Guidelines mailing==~~
	~~Every new user gets the same email and document. Currently it's a .pdf / .odt file.~~
	~~@Willem, include what software can be used by whom under which restrictions.~~

	==Mailing list==		==Mailing list==
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	Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).		Chemdraw licensed to socmoe-access@science.ru.nl (Otherwise ask Dani).

	~~==CCleaner==~~
	~~Needs to be reconfigured per user.~~

	~~Intel rapid storage (icon). If everything is green, good. Drive of identical capacity needs to be installed as the mirror should it fail.~~
	~~Folder on the desktop with maintainance commands.~~
	~~Check SMART overall-health self-assessment test result: PASSED (if not, contact Hakim). Ran for both hard drives. Do this every six months.~~

	==Suggestions from Hakim==		==Suggestions from Hakim==

Wtitulaer at 16:57, 29 January 2025

2025-01-29T16:57:29Z

← Older revision		Revision as of 16:57, 29 January 2025
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	This is an admin maintenance guide for the SOC workstation.		This is an admin maintenance guide for the SOC workstation.

	~~{{Colored box\|title=~~Access to the Station~~\|content=~~To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}		'''Access to the Station''': To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl

	{{{Access to the Station}}}		{{{Access to the Station}}}

Wtitulaer at 16:56, 29 January 2025

2025-01-29T16:56:28Z

← Older revision		Revision as of 16:56, 29 January 2025
Line 1:		Line 1:
	This is an admin maintenance guide for the SOC workstation.		This is an admin maintenance guide for the SOC workstation.

			{{Colored box\|title=Access to the Station\|content=To gain access to the SOC workstation, please contact socmoe-access@science.ru.nl}}

	{{{Access to the Station}}}		{{{Access to the Station}}}

Wtitulaer at 16:55, 29 January 2025

2025-01-29T16:55:07Z

@@ Line 1: / Line 1: @@
 =Maintenance=
-BIOS password lost, but should not be a problem. Physical jumper can circumvent this problem.
+Important to note is that for any problem that should arise, Hakim can be contacted in principle. It also good to note that we no longer know the BIOS password (can be overwritten with a physical jumper) but for now this should not be an issue.
 ==Teamviewer==

Wtitulaer at 14:38, 29 January 2025

2025-01-29T14:38:02Z

@@ Line 1: / Line 1: @@
 =Maintenance=
 ==Teamviewer==
-Privacy black screen
+Privacy black screen.
 Licentiebeheer ILS Wietske (RU), Samuel handels the payment.
@@ Line 11: / Line 16: @@
 - User receives email and makes account
 - Now the user is active and the share can be assigned to the user with a Read-only permission
 ==Booking==
@@ Line 38: / Line 46: @@
 Emails come from MOE License Management
 Text goes into license.dat

Wtitulaer at 13:19, 29 January 2025

2025-01-29T13:19:44Z

@@ Line 1: / Line 1: @@
-==Maintenance==
+=Maintenance=
 ==Teamviewer==
@@ Line 15: / Line 15: @@
 Currently on Hakim's google drive. @Willem, let Hakim know once you take it offline and inform others on new one.
-==Guidelines==
+==Guidelines mailing==
-Every new user gets it. Currently it's a .pdf / .odt file.
+Every new user gets the same email and document. Currently it's a .pdf / .odt file.
 @Willem, include what software can be used by whom under which restrictions.