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Welcome to our wikiIf you are a member of the lab, please see [[Welcome group members]] for more information. This wiki is designed to address several different user [[:Category:Roles|roles]]:  general public users, lab members, curators, developers and sysadmins.
Welcome!  We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the [[Shoichet Lab]] at [[UCSF]].


{{TOCright}}
== Software and Databases ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] ||  Our molecular docking software ||  Latest are [[DOCK 3.7]] and [[DOCK 6.7]]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening
|-
|  [[:Category:ZINC|ZINC]] || Commercially available compounds || [http://zinc.docking.org zinc.docking.org]
|-
|  [[DOCK Blaster]] ||  A public access service for docking screens || [http://blaster.docking.org blaster.docking.org]
|-
|  [[DUDE]] and [[DUD]] || Benchmarks for docking|| [http://dude.docking.org/generate dude.docking.org/generate]
|-
|  [[Aggregator Advisor]] ||A public access database of known aggregators ||  [http://advisor.docking.org advisor.docking.org]
|}
== Other Starting Points ==
{| class="wikitable"
|-
| Topics ||  [[:Category:Systems pharmacology | Systems pharmacology]]  ||  [[:Category:Docking|Molecular Docking]]
|| [[:Category:Aggregation| Colloidal aggregation]] || [[:Category:Model systems | Model systems ]] || [[:Category:Covalent | Covalent docking]]
|-
| Techniques || [[Hit picking party]] || [[DOCK 3.7]] || [[Assaying Compound Activity]] || [[:Category:Tutorials | Tutorials ]]  ||  [[:Category:API | programmatic access (API) ]]
|-
| Enumerations || [[:Category:Software|Software ]] ||  [[:Category:Databases | Databases]]  || [[:Category:Free|Free]] || [[:Category:Freecom|Free to some]] || [[:Category:Commercial|Commercial]]
|-
| Navigation || [[:Category:Topic | Topics ]]  || [[Special:Categories| Categories]] ||  [[:Category:Roles |Roles]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]]
|-
| Other ||  [[:Category:FAQ|FAQ]] || [[Feedback]]  || [[:Category:Problems | Problems]] || [[:Category:Jargon | Jargon]]  ||  [[:Category:Theory |Theory pages]]
|}
= Services =  
= Services =  
We offer many public [[:Category:Services | services]], including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm.
We offer many public [[:Category:Services | services]], including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm.
* [[:Category:API]] - programmatic use of tools not requiring ssh-level access, including iPython Notebook
{{TOCright}}


= Outages =  
= Outages =  
Our servers are up all the time with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, Facebook page http://facebook.com/zincdb and our twitter feed [https://twitter.com/chem4biology @chem4biology].  If there is an unscheduled outage (crash), we will do our best to communicate this via twitter and the blog as soon as possible.  If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461
Our servers are up all the time, with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, which is also available as an RSS feed.  We also try to use our Facebook page http://facebook.com/zincdb and our twitter feed [https://twitter.com/chem4biology @chem4biology] when we remember.  If there is an unscheduled outage (crash), we will do our best to communicate this via our blog as soon as possible.  If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461


= Support  =
= Support  =
Line 15: Line 46:


= Privacy =  
= Privacy =  
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk.
We aim to keep confidential information such as passwords secure, but we can offer no guarantees. You must use these services at your own risk.
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc.docking.org available].
See our [[DISI:Privacy_policy|privacy policy]]. An SSL version of ZINC is [https://zinc.docking.org available].


[[Category:FAQ]]
[[Category:FAQ]]
[[Category:Roles]]
[[Category:Roles]]

Revision as of 05:10, 3 June 2015

Welcome! We hope you find what you are looking for on this wiki, which is focused on software tools for ligand discovery and systems pharmacology, particularly the tools of the Shoichet Lab at UCSF.

Software and Databases

Main article Description Notes/Links
DOCK Our molecular docking software Latest are DOCK 3.7 and DOCK 6.7
SEA Similarity Ensemble Approach Drug repurposing, target identification, phenotypic screening
ZINC Commercially available compounds zinc.docking.org
DOCK Blaster A public access service for docking screens blaster.docking.org
DUDE and DUD Benchmarks for docking dude.docking.org/generate
Aggregator Advisor A public access database of known aggregators advisor.docking.org

Other Starting Points

Topics Systems pharmacology Molecular Docking Colloidal aggregation Model systems Covalent docking
Techniques Hit picking party DOCK 3.7 Assaying Compound Activity Tutorials programmatic access (API)
Enumerations Software Databases Free Free to some Commercial
Navigation Topics Categories Roles Article type Attributes
Other FAQ Feedback Problems Jargon Theory pages

Services

We offer many public services, including software and databases that are free to use and download. For software distributions, for-profit organizations are generally required to obtain a commercial license, e.g. see http://dock.compbio.ucsf.edu/Online_Licensing/index.htm.

Outages

Our servers are up all the time, with rare exceptions. If we must perform maintenance, we will communicate this in advance via our blog http://docking.org, which is also available as an RSS feed. We also try to use our Facebook page http://facebook.com/zincdb and our twitter feed @chem4biology when we remember. If there is an unscheduled outage (crash), we will do our best to communicate this via our blog as soon as possible. If our servers appear down or broken and we have not communicated this, we would be grateful to be told via support at docking.org or +(415) 937-1461

Support

If you have a problem or a question, we always like to hear about it. Please see feedback for how to communicate with us.

Privacy

We aim to keep confidential information such as passwords secure, but we can offer no guarantees. You must use these services at your own risk. See our privacy policy. An SSL version of ZINC is available.