Need help- Why there is network connection
Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu) * Why the network connection is being made and what is the reason behind it? * Is there any sorts of data transfer is being happened from the user system? * Is there any settings in the application to disable the network connections? * If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha
Hi Siddhartha, When Chimera starts up, it may contact www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/> to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences). There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things. There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory). --Eric Eric Pettersen UCSF Computer Graphics Lab
On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> wrote:
Hi,
Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu <http://www.cgl.ucsf.edu/>)
• Why the network connection is being made and what is the reason behind it? • Is there any sorts of data transfer is being happened from the user system? • Is there any settings in the application to disable the network connections? • If users can use the software to export/import data. Is there any cloud service associated with this?
It would be of great help if you can kindly give a clarity for the above network connection ASAP.
Regards, Siddhartha _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users <https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users>
Hi Siddhartha, This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch: <https://www.rbvi.ucsf.edu/chimera/docs/webservices.html> Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Siddhartha, When Chimera starts up, it may contact www.cgl.ucsf.edu to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences). There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things. There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> wrote:
Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
• Connection to 169.230.27.29 on tcp/80 (www.cgl.ucsf.edu)
• Why the network connection is being made and what is the reason behind it? • Is there any sorts of data transfer is being happened from the user system? • Is there any settings in the application to disable the network connections? • If users can use the software to export/import data. Is there any cloud service associated with this?
It would be of great help if you can kindly give a clarity for the above network connection ASAP.
Regards, Siddhartha
Hi Elaine, Good day!! Thanks much for sharing the details. If we need more information, we shall connect you. Thanks much for your help and support in advance. Regards, Siddhartha -----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, April 12, 2021 11:46 PM To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection Hi Siddhartha, This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch: <https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/webservic... > Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Siddhartha, When Chimera starts up, it may contact https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_... to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences). There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things. There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> wrote:
Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
• Connection to https://urldefense.com/v3/__http://169.230.27.29__;!!Dq7g1IpY!10cAOCZatF_dsW... on tcp/80 (https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_... )
• Why the network connection is being made and what is the reason behind it? • Is there any sorts of data transfer is being happened from the user system? • Is there any settings in the application to disable the network connections? • If users can use the software to export/import data. Is there any cloud service associated with this?
It would be of great help if you can kindly give a clarity for the above network connection ASAP.
Regards, Siddhartha
Thank you for the explanation, That as really insightful and helped me gain a better understanding of data transfer, blasting, and where/how processing of certain tasks are done. Everyone in the Chimera program is doing great work and your support is top notch! You are all deeply appreciated. Warmly, Dylan Ramirez On Tue, Apr 13, 2021, 10:35 AM Siddhartha Pradhan (Contractor) < siddhartha.pradhan1@gilead.com> wrote:
Hi Elaine,
Good day!! Thanks much for sharing the details. If we need more information, we shall connect you.
Thanks much for your help and support in advance.
Regards, Siddhartha
-----Original Message----- From: Elaine Meng <meng@cgl.ucsf.edu> Sent: Monday, April 12, 2021 11:46 PM To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> Cc: Chimera <chimera-users@cgl.ucsf.edu> Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection
Hi Siddhartha, This page lists the web services (and databases on the web) that may be accessed by Chimera, depending on which features you use and which data you fetch:
< https://urldefense.com/v3/__https://www.rbvi.ucsf.edu/chimera/docs/webservic...
Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Apr 12, 2021, at 11:00 AM, Eric Pettersen <pett@cgl.ucsf.edu> wrote:
Hi Siddhartha, When Chimera starts up, it may contact https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_... to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences). There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things. There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory).
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) < siddhartha.pradhan1@gilead.com> wrote:
Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made.
• Connection to https://urldefense.com/v3/__http://169.230.27.29__;!!Dq7g1IpY!10cAOCZatF_dsW... on tcp/80 ( https://urldefense.com/v3/__http://www.cgl.ucsf.edu__;!!Dq7g1IpY!10cAOCZatF_... )
• Why the network connection is being made and what is the reason behind it? • Is there any sorts of data transfer is being happened from the user system? • Is there any settings in the application to disable the network connections? • If users can use the software to export/import data. Is there any cloud service associated with this?
It would be of great help if you can kindly give a clarity for the above network connection ASAP.
Regards, Siddhartha
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hi Eric, Good day!! Thanks much for sharing the details. If we need more information we shall connect you. Thanks you in advance for your help and support. Regards, Siddhartha From: Eric Pettersen <pett@cgl.ucsf.edu> Sent: Monday, April 12, 2021 11:31 PM To: Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com> Cc: chimera-users@cgl.ucsf.edu Subject: [EXTERNAL] Re: [Chimera-users] Need help- Why there is network connection Hi Siddhartha, When Chimera starts up, it may contact www.cgl.ucsf.edu<https://urldefense.com/v3/__http:/www.cgl.ucsf.edu__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaN_idOu24$> to determine if a newer version of Chimera is available and alert the user if there is one. The frequency of checking (including never) is controlled by the "Update check interval" preference setting (Favorites→Preferences). There is no setting in Chimera to disable all outbound network connections, and doing so would significantly reduce Chimera's usefulness. It would not be able to fetch data from publicly available databases such as the PDB and UniProt, be able to convert SMILES strings to structures, and many other things. There are some "cloud services" (really web services) run on CGL's own servers that some Chimera tools are built on and that involve exporting user data and importing results. They are: comparative modeling with MODELLER, BLASTing sequences, and realigning sequences with Clustal Omega or MUSCLE. It is possible to install local versions of all these programs and have Chimera use the locally installed version instead of the web service. As far as SMILES strings could be considered "user data", the strings are sent to external servers to convert into 3D structures. There may be other less-used external services I'm forgetting (Chimera is a big program and I basing this off my memory). --Eric Eric Pettersen UCSF Computer Graphics Lab On Apr 12, 2021, at 12:56 AM, Siddhartha Pradhan (Contractor) <siddhartha.pradhan1@gilead.com<mailto:siddhartha.pradhan1@gilead.com>> wrote: Hi, Before we install any software in our system within Gilead organization, we do the software security assessment. During our assessment for " UCSF Chimera v1.15", we found below external network connection is being made. 1. Connection to 169.230.27.29<https://urldefense.com/v3/__http:/169.230.27.29__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNSBeZYQY$> on tcp/80 (www.cgl.ucsf.edu<https://urldefense.com/v3/__http:/www.cgl.ucsf.edu/__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNhFT045w$>) • Why the network connection is being made and what is the reason behind it? • Is there any sorts of data transfer is being happened from the user system? • Is there any settings in the application to disable the network connections? • If users can use the software to export/import data. Is there any cloud service associated with this? It would be of great help if you can kindly give a clarity for the above network connection ASAP. Regards, Siddhartha _______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu<mailto:Chimera-users@cgl.ucsf.edu> Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users<https://urldefense.com/v3/__https:/plato.cgl.ucsf.edu/mailman/listinfo/chimera-users__;!!Dq7g1IpY!0whzterhb2xtDphhi4yu2Mvi_XujJxs2TtlMIj_mV9E7jEUBideFagaFrPWQ8LaNxBkYCHg$>
participants (4)
-
Dylan Ramir -
Elaine Meng -
Eric Pettersen -
Siddhartha Pradhan (Contractor)