DISI - User contributions [en]

Serge's Services

2026-10-02T20:17:53Z

Sstrizhov:

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - cluster2(epyc:3000). http://10.20.1.42:3000
* datagrok - cluster2(epyc-a40:8090).

* cdk/depict cluster2(abacus:8180). http://10.20.0.5:8180/
* jupyter-hub cluster7(https://cpu02:8888). <a target=_blank href="https://10.70.53.183:8888">cpu02</a>

* dataset-browser cluster2(abacus:8000).
* dataset-browser-dev cluster2(abacus:8010).

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

These steps may require sudo or root permissions as it uses docker!!

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

=== dataset-browser ===
TBD

[[Category:Serge]]

Network Troubleshooting

2026-10-02T19:52:33Z

Sstrizhov:

Last Updated October 2nd, 2026 for Rocky Linux 9.

Note: One of the steps requires administrative access.

=== General First Step ===

1. <b>Install iperf3. This will be your network testing tool.</b>

<syntaxhighlight lang="bash">
sudo dnf install -y iperf3
</syntaxhighlight>

<blockquote>
You can check if it's properly installed by running iperf3 and seeing any output. If it says 'command not found', then it didn't install or doesn't exist.
</blockquote>

=== Server Side (where to test the connection from) ===

2. After installing iperf3, run the following command to start your origin server for testing link speeds. This will need an open port on that machine.

<syntaxhighlight lang="bash">
iperf3 -p {your_port_of_choice} -s
</syntaxhighlight>

=== Client Side (where to test the connection with) ===

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {hostname/local ip of server machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

[[Category:Serge]]

Network Troubleshooting

2026-10-02T19:52:10Z

Sstrizhov:

Network Troubleshooting

2026-10-02T19:51:37Z

Sstrizhov:

Network Troubleshooting

2026-10-02T19:50:29Z

Sstrizhov:

Last Updated October 2nd, 2026 for Rocky Linux 9.

Note: One of the steps requires administrative access.

1. <b>Install iperf3. This will be your network testing tool.</b>

<syntaxhighlight lang="bash">
sudo dnf install -y iperf3
</syntaxhighlight>

=== Server Side (where to test the connection from) ===

2. After installing iperf3, run the following command to start your origin server for testing link speeds. This will need an open port on that machine.

<syntaxhighlight lang="bash">
iperf3 -p {your_port_of_choice} -s
</syntaxhighlight>

=== Client Side (where to test the connection with) ===

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {hostname/local ip of server machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-02T19:50:14Z

Sstrizhov:

Last Updated October 2nd, 2026.

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. <b>Install iperf3. This will be your network testing tool.</b>

<syntaxhighlight lang="bash">
sudo dnf install -y iperf3
</syntaxhighlight>

=== Server Side (where to test the connection from) ===

2. After installing iperf3, run the following command to start your origin server for testing link speeds. This will need an open port on that machine.

<syntaxhighlight lang="bash">
iperf3 -p {your_port_of_choice} -s
</syntaxhighlight>

=== Client Side (where to test the connection with) ===

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {hostname/local ip of server machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-02T19:49:54Z

Sstrizhov:

Last Updated October 2nd, 2026.

=== Steps to Troubleshoot a local connection on a Rocky Linux Machine ===

Note: One of the steps requires administrative access.

1. <b>Install iperf3. This will be your network testing tool.</b>

<syntaxhighlight lang="bash">
sudo dnf install -y iperf3
</syntaxhighlight>

==== Server Side (where to test the connection from) ====

2. After installing iperf3, run the following command to start your origin server for testing link speeds. This will need an open port on that machine.

<syntaxhighlight lang="bash">
iperf3 -p {your_port_of_choice} -s
</syntaxhighlight>

==== Client Side (where to test the connection with) ====

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {hostname/local ip of server machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:25:30Z

Sstrizhov:

=== Steps to Troubleshoot a local connection on a Rocky Linux Machine ===

Note: One of the steps requires administrative access.

1. <b>Install iperf3. This will be your network testing tool.</b>

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:25:06Z

Sstrizhov:

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. <b>Install iperf3. This will be your network testing tool.</b>

2. <b>Run the following command to find the network you want to test.</b>

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. <b>Run ethtool with the name of the network device as an argument.</b>

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. <b>Run ethtool with the '-i' flag to get the lspci slot identifier.</b>

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. <b>Get the LnkSta and LnkCap values from lspci.</b>

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. <b>Run iperf3 to get active network speed data.</b>

<syntaxhighlight lang="bash">
iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:24:08Z

Sstrizhov:

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. Install iperf3. This will be your network testing tool.

2. Run the following command to find the network you want to test.

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. Run ethtool with the name of the network device as an argument.

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. Run ethtool with the '-i' flag to get the lspci slot identifier.

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. Get the LnkSta and LnkCap values from lspci.

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. Run iperf3 to get active network speed data.

<syntaxhighlight lang="bash">
iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:23:44Z

Sstrizhov: more changes

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. Install iperf3. This will be your network testing tool.

2. Run the following command and look at the network you want to test.

<syntaxhighlight lang="bash">
ifconfig
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. Run ethtool with the name of the network device as an argument.

<syntaxhighlight lang="bash">
ethtool {network device name}
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. Run ethtool with the '-i' flag to get the lspci slot identifier.

<syntaxhighlight lang="bash">
ethtool -i {network device name}
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. Get the LnkSta and LnkCap values from lspci.

<syntaxhighlight lang="bash">
sudo lspci -vv -s {bus_info_value} | grep “Lnk”
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. Run iperf3 to get active network speed data.

<syntaxhighlight lang="bash">
iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:23:11Z

Sstrizhov: Prettier text

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. Install iperf3. This will be your network testing tool.

2. Run the following command and look at the network you want to test.

<syntaxhighlight lang="bash">
`ifconfig`
</syntaxhighlight>

<blockquote>
Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).
</blockquote>

3. Run ethtool with the name of the network device as an argument.

<syntaxhighlight lang="bash">
`ethtool {network device name}`
</syntaxhighlight>

example: `ethtool eno2`

<blockquote>
Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!
</blockquote>

4. Run ethtool with the '-i' flag to get the lspci slot identifier.

<syntaxhighlight lang="bash">
`ethtool -i {network device name}`
</syntaxhighlight>

example: `ethtool -i eno2`

<blockquote>
Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.
</blockquote>

5. Get the LnkSta and LnkCap values from lspci.

<syntaxhighlight lang="bash">
`sudo lspci -vv -s {bus_info_value} | grep “Lnk”`
</syntaxhighlight>

<blockquote>
The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.
</blockquote>

6. Run iperf3 to get active network speed data.

<syntaxhighlight lang="bash">
`iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30`
</syntaxhighlight>

<blockquote>
All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s
</blockquote>

Network Troubleshooting

2026-10-01T21:18:31Z

Sstrizhov: Documenting network testing.

== Steps to Troubleshoot a local connection on a Rocky Linux Machine ==

Note: One of the steps requires administrative access.

1. Install iperf3. This will be your network testing tool.

2. Run the following command and look at the network you want to test.

`ifconfig`

Local networks general start with `10.`, for example, `10.70.***.**`. Pick the relevant one to test and copy it's network device name (such as eno2).

3. Run ethtool with the name of the network device as an argument.

`ethtool {network device name}`

example: `ethtool eno2`

Check the 'speed' variable. This is how fast that network device is made to be. NOTE: This is in gigaBITS, not gigaBYTES. One gigabyte is eight gigabits, so keep this in mind!

4. Run ethtool with the '-i' flag to get the lspci slot identifier.

`ethtool -i {network device name}`

example: `ethtool -i eno2`

Here, you want to copy the last six numbers of 'bus info'. For example, if your bus info is 0000:65:00.1, you just copy '65:00.1'.

5. Get the LnkSta and LnkCap values from lspci.

`sudo lspci -vv -s {bus_info_value} | grep “Lnk”`

The LnkSta value (in GT/s) shows you how fast the PCI port is, and LnkCap shows you how fast it can go. When things are perfect, these two values should be the same.

6. Run iperf3 to get active network speed data.

`iperf3 -c {chosen testing machine} -P 4 -p {port of machine} -t 30`

All the data we've gathered earlier is data in theory. With this, we can actively test the actual network speed between our systems.

The speed can be a little less than what's shown on ethtool, that's normal. For example, a network device may display having speeds of 10Gbi/s but in actuality it's closer to 9.40Gbi/s

SDF to SMI

2026-09-21T18:27:03Z

Sstrizhov:

=== Openbabel Method (Cluster 7) ===

go on cluster7 and run the following

<syntaxhighlight lang="bash">
ml anaconda3
conda create -n obabel conda-forge::openbabel -y
conda activate obabel
</syntaxhighlight>

This should make you your own conda env with openbabel installed. Then, for conversion..

<syntaxhighlight lang="bash">
obabel <input_path>.sdf -O <output_path>.smi
</syntaxhighlight>

[[Category:Serge]]

SDF to SMI

2026-09-21T18:26:06Z

Sstrizhov: new page

### Openbabel Method (Cluster 7)

go on cluster7 and run the following

<syntaxhighlight lang="bash">
ml anaconda3
conda create -n obabel conda-forge::openbabel -y
conda activate obabel
</syntaxhighlight>

This should make you your own conda env with openbabel installed. Then, for conversion..

<syntaxhighlight lang="bash">
obabel <input_path>.sdf -O <output_path>.smi
</syntaxhighlight>

[[Category:Serge]]

Serge's Services

2026-09-11T21:08:16Z

Sstrizhov:

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - cluster2(epyc:3000). http://10.20.1.42:3000
* datagrok - cluster2(epyc-a40:8090).

* cdk/depict cluster2(abacus:8180). http://10.20.0.5:8180/
* jupyter-hub cluster7(https://cpu02:8888). <a target=_blank href="https://10.70.53.183:8888">cpu02</a>

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

These steps may require sudo or root permissions as it uses docker!!

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

Serge's Services

2026-09-11T19:32:29Z

Sstrizhov:

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - cluster2(epyc:3000). http://10.20.1.42:3000
* datagrok - cluster2(currently down). http://10.20.1.42:8080

* cdk/depict cluster2(abacus:8180). http://10.20.0.5:8180/
* jupyter-hub cluster7(https://cpu02:8888). <a target=_blank href="https://10.70.53.183:8888">cpu02</a>

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

These steps may require sudo or root permissions as it uses docker!!

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

Serge's Services

2026-09-11T18:42:41Z

Sstrizhov: update

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - cluster2(epyc:3000)
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8180)
* jupyter-hub cluster7(https://cpu02:8888)

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

These steps may require sudo or root permissions as it uses docker!!

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

How to create a vpn/ssh tunnel

2026-09-10T18:07:36Z

Sstrizhov: adding a macof ssh fix

= Generating an SSH key =
First, copy this command into your terminal to start generating a new ssh key.

ssh-keygen -t rsa

It will then request you to specify a location.

Enter file in which to save the key (/Users/user/.ssh/id_rsa): <input optional pathway here>

If you do not insert a path, it will instead default to the location specified (default ie: /Users/user/.ssh/id_rsa). If you already have a key made, then it will ask you whenever you want to overwrite it or not. If you are using that key for something else, then make the new one at a different path location.
Lastly, it will ask you for a passphrase, which is optional.

Enter passphrase (empty for no passphrase): <input optional passphrase here>

Your public ssh key can be found in the location where you specified earlier inside a hidden folder (default ie: /Users/user/.ssh/bkslab_key.pub)
Send it to the person who creates your account, so they can add it into portal.

= Direct Connection =
=== Remote Connection ===
'''portal3 is just the lobby, there is nothing there. Inside portal3, you have to open doors to gimel OR epyc OR gimel2'''
<source> ssh <username>@portal3.compbio.ucsf.edu </source>

THEN

<source> ssh <username>@<epyc OR gimel OR gimel2> </source>

=== Local Connection ===
<source> ssh <username>@gimel.compbio.ucsf.edu </source>

= Making a portal and tunnel =

=== Linux/MacOS ===
<blockquote>
<b>WARNING!</b> If you are SSHing on MacOS, your SSH connection will be automatically terminated after some time of inactivity. To prevent that from happening, open the following file:

<code>vim ~/.ssh/config</code>

Then add the following to the start of the file:

<syntaxhighlight lang="bash">
Host *
ServerAliveInterval 60
ServerAliveCountMax 2
</syntaxhighlight>

This should prevent it from closing the SSH connection as long as you maintain an internet connection.
</blockquote>

First, open two terminals. In the first terminal, type the following:

ssh <options/flags> localhost:2222:epyc2:22 -D1080 portal3.ucsf.bkslab.org -l <username>

Example:

ssh -vCL localhost:2222:epyc2:22 -D1080 portal3.ucsf.bkslab.org -l jjg

This terminal will act as your 'portal'. You can't do much with the portal until you make a tunnel.

In the second terminal, type:

ssh -oHostKeyAlgorithms=+ssh-rsa -p 2222 <username>@localhost

Example:

ssh -oHostKeyAlgorithms=+ssh-rsa -p 2222 jj@localhost

This should create a tunnel. To see if you logged in, try running the command 'hostname'. If it's successful, then you are in!

___

Here's another example, say ''you want to scp files directly from your laptop to your home directory on gimel.''

First open two terminals. In one terminal type the following:

ssh <options/flags> localhost:2222:epyc2:22 -D1080 portal3.ucsf.bkslab.org -l <username>
ssh -vCL localhost:2222:epyc2:22 -D1080 portal3.ucsf.bkslab.org -l jjg

In the other terminal type:

scp -P 2222 file_you_want_to_copy <username>@localhost:~

=== Troubleshooting for Mac ===
If you see this error:
Unable to negotiate with 169.230.26.166 port 22: no matching host key type found. Their offer: ssh-rsa,ssh-dss

Solutions:

Option 1:
Add '-oHostKeyAlgorithms=+ssh-rsa' flag in your ssh/scp command

Option 2:
vim ~/.ssh/config
Edit config file with the correct values
Host <hostname>
HostName <hostname>
Port <your_port>
User <username>
ServerAliveInterval 100
HostKeyAlgorithms +ssh-rsa
PubkeyAcceptedKeyTypes +ssh-rsa

=== Windows OS ===

Open putty.exe and select the session that you want to use as a ssh tunnel (ie portal.uoft.bkslab.org).

Then click on Connection -> SSH -> tunnels

In Source Port enter 1080 (or any port above 1024).

Then click the Dynamic button and then click Add.

It should look like this:

[[File:proxy1.png]]

Then go back to Session and click Save.

Then download the "standard" version of FoxyProxy here: http://getfoxyproxy.org/downloads.html

Once you’ve downloaded it there should be a little fox picture next to the url bar (upper right hand corner of web browser). Click on that little picture and select Options from the dropdown list.

You should see this:

[[File:foxy1.png]]

Click on Add New Proxy

Then click on the General tab.

Enter a proxy name and then select the Proxy Details tab.

Enter “localhost” in “Host or IP Address” and 1080 for “Port” (or whatever port number you entered in putty).

Click the “SOCKS proxy?” Button and make sure the “SOCKS v5” button is also clicked.

Your screen should look like this:

[[File:foxy2.png]]

Then click Save.

Then click on the fox again on the upper right hand corner and click on “Us proxy whatever_you_named_it Proxy for all URLs”

Then click on putty and open your session. A terminal will pop up and ask for your passphrase. Enter your passphrase (for your ssh key). That’s it!

To test if your tunnel is good, go to: http://whatismyipaddress.com/

This will tell you what ip address you have. If it says the IP address of the remote host you're connecting to in putty, you are good to go! :)

This session will remain open as long as your ssh putty session is open.

'''To scp files in Windows''' through this ssh tunnel, download WinSCP here: http://winscp.net/download/winscp551setup.exe

Once it finishes downloading, run it and go through all the prompts. You can (if you want) to import all your existing sessions from putty, but it’s really not necessary.

Once it’s done, open it.

Click on “New Site”.

Then, in the File protocol drop down menu, select SCP.

In Host name, put the host name or IP address of the machine you want to transfer files to.

Keep the port number as 22. It should look something like this:

[[File:scp1.png]]

Then click on Advanced -> Connection -> Proxy

Click on the “Proxy type” drop down menu and select SOCKS5.

For “Proxy host name” write localhost. Make the port number 1080 (or whatever port you chose to use in putty).

it should look like this:

[[File:scp2.png]]

Click OK, then Save.

It will prompt you to enter a name, call it whatever makes sense to you.

Assuming that your putty session is still open, click Login.

It should prompt you to enter your username and password in the bottom.

You should then see a screen that looks like this:

[[File:scp3.png]]

To transfer files from one to the other, select the file that you want to transfer and then click “Upload” to transfer files to the server and then specify which folder you want to save it to. If you are downloading files from the server to your computer, click the file you want to download and then click “Download” and specify where you want to download it to.

To exit, click on session -> disconnect

'''When you are done''' with your vpn session, exit from the ssh putty session (type exit on the terminal screen).

Then, on your browser, click on the little fox in the upper right hand corner and select “Disable FoxyProxy”.

[[Category:Tutorials]]
[[Category:Internal]]

Serge's Services

2026-09-02T18:40:12Z

Sstrizhov: little syntax fix

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - TBD
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8180)
* jupyter-hub cluster7(https://cpu02:8888)

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

These steps may require sudo or root permissions as it uses docker!!

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

Serge's Services

2026-09-02T18:39:31Z

Sstrizhov: adding a little bit of qsar info

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - TBD
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8180)
* jupyter-hub cluster7(https://cpu02:8888)

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

**These steps may require sudo or root permissions as it uses docker!!**

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ===
Fresh installation guide for cluster 7: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

Serge's Services

2026-09-02T18:36:35Z

Sstrizhov: qsar

== These are the services that I'm running as of September 2nd, 2026. ==

* qsar - cluster2(epyc:4545)
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8180)
* jupyter-hub cluster7(https://cpu02:8888)

== How to start a service manually ==
Do this if you can't perform it through gitlab automation tools or if the tools don't exist yet.

**These steps may require sudo or root permissions as it uses docker!!**

=== Jupyter-Hub ===

1. Log into cluster 7 (login01) and SSH into a cpu node:

<syntaxhighlight lang="bash">
ssh <username>@169.230.26.173
ssh cpu02
</syntaxhighlight>

You can use a different node than cpu02. Discover nodes by using sinfo.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S jupyter-hub
</syntaxhighlight>

3. Navigate to the following folder while in the screen (you should automatically be in it):

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/jupyter-hub
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

This should automatically build and get the docker container running for you at "https://cpu02:8888" unless 8888 as a socket is already in use.

=== cdk/depict ===
1. Log into cluster 2.

2. Create a screen so that the software works when you log off.

<syntaxhighlight lang="bash">
screen -S cdkdepict
</syntaxhighlight>

3. Navigate the following folder:

<syntaxhighlight lang="bash">
/nfs/home/sstrizhov/code/depict/docker
</syntaxhighlight>

4. Run the following script (may need sudo):

<syntaxhighlight lang="bash">
./startup.sh
</syntaxhighlight>

=== Qsar ====
Fresh installation guide: https://wiki.docking.org/index.php?title=Qsar

[[Category:Serge]]

Serge's Services

2026-09-02T18:10:31Z

Sstrizhov: cdkdepict guide

Serge's Services

2026-09-02T17:48:27Z

Sstrizhov: updated code blocks

Serge's Services

2026-09-02T17:47:21Z

Sstrizhov: testing new code block

Serge's Services

2026-09-02T17:45:53Z

Sstrizhov: testing newline

Serge's Services

2026-09-02T17:45:33Z

Sstrizhov: jupyterhub instructions

Serge's Services

2026-09-02T17:38:42Z

Sstrizhov: adding some guidelines

Serge's Services

2026-08-31T17:49:50Z

Sstrizhov: /* These are the services that I'm running as of July 17th, 2026. */

=== These are the services that I'm running as of July 17th, 2026. ===

* qsar - cluster2(epyc:4545)
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8180)
* jupyter-hub cluster7(https://cpu02:8888)

[[Category:Serge]]

Serge's Services

2026-08-31T17:10:05Z

Sstrizhov: /* These are the services that I'm running as of July 17th, 2026. */

=== These are the services that I'm running as of July 17th, 2026. ===

* qsar - cluster2(epyc:4545)
* datagrok - cluster2(epyc:8080)

* cdk/depict cluster2(abacus:8081)
* jupyter-hub cluster7(https://cpu02:8888)

[[Category:Serge]]

DOCK 3.8:How to install pydock3

2026-08-25T18:49:55Z

Sstrizhov: more detail to instructions.

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

<code>git clone https://github.com/docking-org/pydock3</code>

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

<code>conda create -n your_env_name python=3.8</code>

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.

<code>conda activate your_env_name</code>

<code>pip install -e pydock3</code>

4. Check if it is installed by running the following in a folder of your choice. This will create a new folder named 'blastermaster_job' if successful.

<code>pydock3 blastermaster - new</code>

If the above runs without error, then it's installed. Navigate to [[Blastermaster (pydock3 script)]] for instructions on how to use this software.

'''Note:''' requires Python>=3.8

[[Category:DOCK 3.8]]

DOCK 3.8:How to install pydock3

2026-08-25T18:47:33Z

Sstrizhov: one LAST syntax update hopefully

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

<code>git clone https://github.com/docking-org/pydock3</code>

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

<code>conda create -n your_env_name python=3.8</code>

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.

<code>conda activate your_env_name</code>

<code>pip install -e pydock3</code>

'''Note:''' requires Python>=3.8

[[Category:DOCK 3.8]]

DOCK 3.8:How to install pydock3

2026-08-25T18:47:06Z

Sstrizhov: another syntax update

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

<code>git clone https://github.com/docking-org/pydock3</code>

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

<code>conda create -n your_env_name python=3.8</code>

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.

<code>conda activate your_env_name
pip install -e pydock3</code>

'''Note:''' requires Python>=3.8

[[Category:DOCK 3.8]]

DOCK 3.8:How to install pydock3

2026-08-25T18:46:46Z

Sstrizhov: updated syntax of code blocks

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

<code>git clone https://github.com/docking-org/pydock3</code>

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

<code>conda create -n your_env_name python=3.8</code>

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.
<code>conda activate your_env_name
pip install -e pydock3</code>

'''Note:''' requires Python>=3.8

[[Category:DOCK 3.8]]

DOCK 3.8:How to install pydock3

2026-08-25T18:45:40Z

Sstrizhov: updated installation instructions

[[pydock3]] is a Python package wrapping the [[DOCK|DOCK Fortran program]] that provides tools to help standardize and automate the computational methods employed in molecular docking.

Note: if you are at UCSF on gimel or wynton, you do not need to install, the software is already locally maintained.

== Instructions ==
1. git clone the following repo: https://github.com/docking-org/pydock3 into a folder of your choice. Navigate to the folder first before cloning.

```git clone https://github.com/docking-org/pydock3```

2. Now that you have a new folder called pydock3, create a new conda environment to install packages into. Make sure it has python version>=3.8. Replace 'your_env_name' with your chosen environment name.

```conda create -n your_env_name python=3.8```

3. Activate the conda environment and install pydock3 onto it with pip. Do not cd into the pydock3 folder itself before running pip.
```conda activate your_env_name
pip install -e pydock3```

'''Note:''' requires Python>=3.8

[[Category:DOCK 3.8]]

Serge's Services

2026-07-17T19:09:52Z

Sstrizhov: me

=== These are the services that I'm running as of July 17th, 2026. ===

* qsar - (epyc:4545)
* datagrok - (epyc:8080)

[[Category:Serge]]

Serge's Services

2026-07-17T19:07:49Z

Sstrizhov: create

=== These are the services that I'm running as of July 17th, 2026. ===

* qsar - (epyc:4545)
* datagrok - (epyc:8080)

Qsar

2026-07-09T20:01:21Z

Sstrizhov: Creating qsar guide.

== Synopsis ==

This guide will detail the installation and usage of Qsar (https://github.com/syedzayyan/qsar-in-browser) on cluster 7.

Last updated on July 9th, 2026. Things may change with time, so don't trust this guide after a long time has passed.

== Installation and Running ==

First, clone the Qsar repo off of github into your chosen folder and cd into it.

<code>
git clone https://github.com/syedzayyan/qsar-in-browser.git

cd qsar-in-browser
</code>

Then, create a new conda environment followed by a nodejs installation after loading anaconda3.

<code>
ml anaconda3

conda create -n qsar

conda activate qsar

conda install conda-forge::nodejs
</code>

Finally, install the dependencies and run the website.

<code>
npm install

npm run dev
</code>

This will start qsar on http://localhost:3000 of the machine that you've started it on.

You may now use an SSH portal and a browser proxy add-on such as SwitchyOmega to remotely connect to the localhost website. If you don't know how to do so, follow the relevant guides on this wiki or ask a lab member.

Create new user

2026-06-23T21:07:01Z

Sstrizhov:

===Identify a UID===
'''Check if a uid that is not taken by any other users'''. Start from 15***
On CentOS 6
$ getent passwd | grep 15***
On CentOS 7
$ id 15***

===Create users and superuser on the LDAP GUI:===
Make sure you turn on Switchy Omega
https://ds.ucsf.bkslab.org/ldapadmin/cmd.php

If you are seeing this error message
You cannot visit ds.ucsf.bkslab.org right now because the website uses HSTS. Network errors and attacks are usually temporary, so this page will probably work later.
You will need to delete 'bkslab.org' domain from your 'Domain security policies' in Chrome
chrome://net-internals/#hsts

====To create a visitor: ====
Click OU=Visitors
Click Create new entry here
Select Generic: User Account
Fill in appropriate sections
-home dir should be /nfs/home/<username>
-password should be encrypted with sha512
-group should be visitors
Keep the uid LDAP suggested and edit in the one you picked later.

==== Create User's Home Directory ====
Log in as root on **mem**
$ sh /export/home/[create-visitor.sh/create-member.sh] <user_name>

=== Generate ssh for login ===
====Create ssh key ====
In the user's home directory's personal computer:
$ ssh keygen

==== Add user's public key to Portal ====
$ ssh portal3 (from a different cluster bit like epyc)
$ sudo -i
$ cd /opt/keys/users
$ vim <username>
Copy the .rsa_key.pub content into the file

==== Add user into Portal ====
On LDAP Admin
Choose ''' dc=bkslab,dc=org (17)''' > '''Groups''' > '''Portal'''
Enter <username> in Add Value

==== Add user into SLURM ====
On gimel2 as a super user:
sudo sacctmgr create user name=<username> account=bks

=== Add s_ user in alpha ===
Since Alpha was created before ldap admin system, new user must be created individually on this machine.

Add the s_ user in
vim /etc/passwd
vim /etc/group

Change password
passwd s_<user>

[[Category: Ben]] [[Category:Sysadmin]]

Create new user

2026-06-23T21:03:59Z

Sstrizhov:

===Identify a UID===
'''Check if a uid that is not taken by any other users'''. Start from 15***
On CentOS 6
$ getent passwd | grep 15***
On CentOS 7
$ id 15***

===Create users and superuser on the LDAP GUI:===
Make sure you turn on Switchy Omega
https://ds.ucsf.bkslab.org/ldapadmin/cmd.php

If you are seeing this error message
You cannot visit ds.ucsf.bkslab.org right now because the website uses HSTS. Network errors and attacks are usually temporary, so this page will probably work later.
You will need to delete 'bkslab.org' domain from your 'Domain security policies' in Chrome
chrome://net-internals/#hsts

====To create a visitor: ====
Click OU=Visitors
Click Create new entry here
Select Generic: User Account
Fill in appropriate sections
-home dir should be /nfs/home/<username>
-password should be encrypted with sha512
-group should be visitors
Keep the uid LDAP suggested and edit in the one you picked later.

==== Create User's Home Directory ====
Log in as root on **mem**
$ sh /export/home/[create-visitor.sh/create-member.sh] <user_name>

=== Generate ssh for login ===
====Create ssh key ====
In the user's home directory's personal computer:
$ ssh keygen

==== Add user's public key to Portal ====
$ ssh portal3 (from a different cluster bit like epyc)
$ sudo -i
$ cd /opt/keys/users
$ vim <username>
Copy the .rsa_key.pub content into the file

==== Add user into Portal ====
On LDAP Admin
Choose ''' dc=bkslab,dc=org (17)''' > '''Groups''' > '''Portal'''
Enter <username> in Add Value

==== Add user into SLURM ====
sudo sacctmgr create user name=<username> account=bks

=== Add s_ user in alpha ===
Since Alpha was created before ldap admin system, new user must be created individually on this machine.

Add the s_ user in
vim /etc/passwd
vim /etc/group

Change password
passwd s_<user>

[[Category: Ben]] [[Category:Sysadmin]]

Create new user

2026-06-23T21:03:49Z

Sstrizhov:

===Identify a UID===
'''Check if a uid that is not taken by any other users'''. Start from 150**
On CentOS 6
$ getent passwd | grep 15***
On CentOS 7
$ id 15***

===Create users and superuser on the LDAP GUI:===
Make sure you turn on Switchy Omega
https://ds.ucsf.bkslab.org/ldapadmin/cmd.php

If you are seeing this error message
You cannot visit ds.ucsf.bkslab.org right now because the website uses HSTS. Network errors and attacks are usually temporary, so this page will probably work later.
You will need to delete 'bkslab.org' domain from your 'Domain security policies' in Chrome
chrome://net-internals/#hsts

====To create a visitor: ====
Click OU=Visitors
Click Create new entry here
Select Generic: User Account
Fill in appropriate sections
-home dir should be /nfs/home/<username>
-password should be encrypted with sha512
-group should be visitors
Keep the uid LDAP suggested and edit in the one you picked later.

==== Create User's Home Directory ====
Log in as root on **mem**
$ sh /export/home/[create-visitor.sh/create-member.sh] <user_name>

=== Generate ssh for login ===
====Create ssh key ====
In the user's home directory's personal computer:
$ ssh keygen

==== Add user's public key to Portal ====
$ ssh portal3 (from a different cluster bit like epyc)
$ sudo -i
$ cd /opt/keys/users
$ vim <username>
Copy the .rsa_key.pub content into the file

==== Add user into Portal ====
On LDAP Admin
Choose ''' dc=bkslab,dc=org (17)''' > '''Groups''' > '''Portal'''
Enter <username> in Add Value

==== Add user into SLURM ====
sudo sacctmgr create user name=<username> account=bks

=== Add s_ user in alpha ===
Since Alpha was created before ldap admin system, new user must be created individually on this machine.

Add the s_ user in
vim /etc/passwd
vim /etc/group

Change password
passwd s_<user>

[[Category: Ben]] [[Category:Sysadmin]]

Create new user

2026-06-23T21:03:26Z

Sstrizhov: updates instructions

===Identify a UID===
'''Check if a uid that is not taken by any other users'''. Start from 150**
On CentOS 6
$ getent passwd | grep 150**
On CentOS 7
$ id 150**

===Create users and superuser on the LDAP GUI:===
Make sure you turn on Switchy Omega
https://ds.ucsf.bkslab.org/ldapadmin/cmd.php

If you are seeing this error message
You cannot visit ds.ucsf.bkslab.org right now because the website uses HSTS. Network errors and attacks are usually temporary, so this page will probably work later.
You will need to delete 'bkslab.org' domain from your 'Domain security policies' in Chrome
chrome://net-internals/#hsts

====To create a visitor: ====
Click OU=Visitors
Click Create new entry here
Select Generic: User Account
Fill in appropriate sections
-home dir should be /nfs/home/<username>
-password should be encrypted with sha512
-group should be visitors
Keep the uid LDAP suggested and edit in the one you picked later.

==== Create User's Home Directory ====
Log in as root on **mem**
$ sh /export/home/[create-visitor.sh/create-member.sh] <user_name>

=== Generate ssh for login ===
====Create ssh key ====
In the user's home directory's personal computer:
$ ssh keygen

==== Add user's public key to Portal ====
$ ssh portal3 (from a different cluster bit like epyc)
$ sudo -i
$ cd /opt/keys/users
$ vim <username>
Copy the .rsa_key.pub content into the file

==== Add user into Portal ====
On LDAP Admin
Choose ''' dc=bkslab,dc=org (17)''' > '''Groups''' > '''Portal'''
Enter <username> in Add Value

==== Add user into SLURM ====
sudo sacctmgr create user name=<username> account=bks

=== Add s_ user in alpha ===
Since Alpha was created before ldap admin system, new user must be created individually on this machine.

Add the s_ user in
vim /etc/passwd
vim /etc/group

Change password
passwd s_<user>

[[Category: Ben]] [[Category:Sysadmin]]

Main Page

2025-05-09T18:41:38Z

Sstrizhov:

<div id="mainpage"></div>__NOTOC__
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles | constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. lala

If you are a <b>new member of a lab</b>, please follow the [[Welcome group members | following guide]].

Documentation [https://docs.docking.org docs.docking.org]

=== Relevant Links ===
* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]
* [[:Category:News | News]]
* [[Group Meeting | Group Meeting Times]]
* [https://x.com/chem4biology/ Outages and Updates]
* [https://discord.gg/4MpD6UF5AN Chat on Discord]

== Are you new here? ==
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We work in five major technology areas:
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]). [[DOCK]]
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties. [[Smallworld]] and [[Arthor]].
* 3) '''Target prediction'''. Given a molecule, our program [[SEA]] can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").
* 4) '''Bespoke Chemistry'''. The [[Chemistry Commons]] is a platform to help chemists and biologist to collaborate. This system allows chemists to define which molecules their new chemistry can access, and it allows biologists to search through this novel bespoke chemistry.
* 5) '''Chemical Libraries'''. [[ZINC]] is available for download in 2D and 3D.

We hope you find this website interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.

== Products ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org]
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons]
|-
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}

== Topics ==
{| class="wikitable"
|-
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]]
|| [[Hit picking party]]
|-
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]]
|-
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] ||  
|}

== Other topics ==
{| class="wikitable"
|-
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]]
|-
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]]
|-
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]]
|}

== Organizational ==
{| class="wikitable"
|-
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]]
|-
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]]
|}

Still haven't found what you're looking for? Try the search bar top right to see if that works...

= Outages and Support =
* We communicate about outages and updates via [https://twitter.com/chem4biology X].
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server]
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937 one four six one
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
* More about ways to [[feedback | communicate with us]].
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free.

= Policies, Privacy and all that =
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]].

[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]

MediaWiki:Bottom-notice-ns-0

2025-03-21T21:22:13Z

Sstrizhov: Sstrizhov moved page Notice-ns to MediaWiki:Bottom-notice-ns-0 without leaving a redirect

<div style="margin-left: 1em; border: 1px solid #1DA0E7; background: #B3DDF4;">'''''Welcome to this wiki!'''''</div>

MediaWiki:Bottom-notice-ns-0

2025-03-21T21:17:47Z

Sstrizhov: Created page with "<div style="margin-left: 1em; border: 1px solid #1DA0E7; background: #B3DDF4;">'''''Welcome to this wiki!'''''</div>"

<div style="margin-left: 1em; border: 1px solid #1DA0E7; background: #B3DDF4;">'''''Welcome to this wiki!'''''</div>

How to create a vpn/ssh tunnel

2025-03-07T20:06:17Z

Sstrizhov: updated command

= Generating an SSH key =
First, copy this command into your terminal to start generating a new ssh key.

ssh-keygen -t rsa

It will then request you to specify a location.

Enter file in which to save the key (/Users/user/.ssh/id_rsa): <input optional pathway here>

If you do not insert a path, it will instead default to the location specified (default ie: /Users/user/.ssh/id_rsa). If you already have a key made, then it will ask you whenever you want to overwrite it or not. If you are using that key for something else, then make the new one at a different path location.
Lastly, it will ask you for a passphrase, which is optional.

Enter passphrase (empty for no passphrase): <input optional passphrase here>

Your public ssh key can be found in the location where you specified earlier inside a hidden folder (default ie: /Users/user/.ssh/bkslab_key.pub)
Send it to the person who creates your account, so they can add it into portal.

= Direct Connection =
=== Remote Connection ===
'''portal3 is just the lobby, there is nothing there. Inside portal3, you have to open doors to gimel OR epyc OR gimel2'''
<source> ssh <username>@portal3.compbio.ucsf.edu </source>

THEN

<source> ssh <username>@<epyc OR gimel OR gimel2> </source>

=== Local Connection ===
<source> ssh <username>@gimel.compbio.ucsf.edu </source>

= Making a portal and tunnel =

=== Linux/MacOS ===

First, open two terminals. In the first terminal, type the following:

ssh <options/flags> localhost:2222:gimel:22 -D1080 portal3.ucsf.bkslab.org -l <username>

Example:

ssh -vCL localhost:2222:gimel:22 -D1080 portal3.ucsf.bkslab.org -l jjg

This terminal will act as your 'portal'. You can't do much with the portal until you make a tunnel.

In the second terminal, type:

ssh -oHostKeyAlgorithms=+ssh-rsa -p 2222 <username>@localhost

Example:

ssh -oHostKeyAlgorithms=+ssh-rsa -p 2222 jj@localhost

This should create a tunnel. To see if you logged in, try running the command 'hostname'. If it's successful, then you are in!

___

Here's another example, say ''you want to scp files directly from your laptop to your home directory on gimel.''

First open two terminals. In one terminal type the following:

ssh <options/flags> localhost:2222:gimel:22 -D1080 portal3.ucsf.bkslab.org -l <username>
ssh -vCL localhost:2222:gimel:22 -D1080 portal3.ucsf.bkslab.org -l jjg

In the other terminal type:

scp -P 2222 file_you_want_to_copy <username>@localhost:~

=== Troubleshooting for Mac ===
If you see this error:
Unable to negotiate with 169.230.26.166 port 22: no matching host key type found. Their offer: ssh-rsa,ssh-dss
Please follow this article to fix it :
https://www.iclarified.com/87910/how-to-fix-no-matching-host-key-type-found-on-mac

=== Windows OS ===

Open putty.exe and select the session that you want to use as a ssh tunnel (ie portal.uoft.bkslab.org).

Then click on Connection -> SSH -> tunnels

In Source Port enter 1080 (or any port above 1024).

Then click the Dynamic button and then click Add.

It should look like this:

[[File:proxy1.png]]

Then go back to Session and click Save.

Then download the "standard" version of FoxyProxy here: http://getfoxyproxy.org/downloads.html

Once you’ve downloaded it there should be a little fox picture next to the url bar (upper right hand corner of web browser). Click on that little picture and select Options from the dropdown list.

You should see this:

[[File:foxy1.png]]

Click on Add New Proxy

Then click on the General tab.

Enter a proxy name and then select the Proxy Details tab.

Enter “localhost” in “Host or IP Address” and 1080 for “Port” (or whatever port number you entered in putty).

Click the “SOCKS proxy?” Button and make sure the “SOCKS v5” button is also clicked.

Your screen should look like this:

[[File:foxy2.png]]

Then click Save.

Then click on the fox again on the upper right hand corner and click on “Us proxy whatever_you_named_it Proxy for all URLs”

Then click on putty and open your session. A terminal will pop up and ask for your passphrase. Enter your passphrase (for your ssh key). That’s it!

To test if your tunnel is good, go to: http://whatismyipaddress.com/

This will tell you what ip address you have. If it says the IP address of the remote host you're connecting to in putty, you are good to go! :)

This session will remain open as long as your ssh putty session is open.

'''To scp files in Windows''' through this ssh tunnel, download WinSCP here: http://winscp.net/download/winscp551setup.exe

Once it finishes downloading, run it and go through all the prompts. You can (if you want) to import all your existing sessions from putty, but it’s really not necessary.

Once it’s done, open it.

Click on “New Site”.

Then, in the File protocol drop down menu, select SCP.

In Host name, put the host name or IP address of the machine you want to transfer files to.

Keep the port number as 22. It should look something like this:

[[File:scp1.png]]

Then click on Advanced -> Connection -> Proxy

Click on the “Proxy type” drop down menu and select SOCKS5.

For “Proxy host name” write localhost. Make the port number 1080 (or whatever port you chose to use in putty).

it should look like this:

[[File:scp2.png]]

Click OK, then Save.

It will prompt you to enter a name, call it whatever makes sense to you.

Assuming that your putty session is still open, click Login.

It should prompt you to enter your username and password in the bottom.

You should then see a screen that looks like this:

[[File:scp3.png]]

To transfer files from one to the other, select the file that you want to transfer and then click “Upload” to transfer files to the server and then specify which folder you want to save it to. If you are downloading files from the server to your computer, click the file you want to download and then click “Download” and specify where you want to download it to.

To exit, click on session -> disconnect

'''When you are done''' with your vpn session, exit from the ssh putty session (type exit on the terminal screen).

Then, on your browser, click on the little fox in the upper right hand corner and select “Disable FoxyProxy”.

[[Category:Tutorials]]
[[Category:Internal]]

Main Page

2025-02-21T18:14:21Z

Sstrizhov:

<div id="mainpage"></div>__NOTOC__
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles | constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic.

If you are a <b>new member of a lab</b>, please follow the [[Welcome group members | following guide]].

=== Relevant Links ===
* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]
* [[:Category:News | News]]
* [https://x.com/chem4biology/ Outages and Updates]
* [https://discord.gg/4MpD6UF5AN Chat on Discord]

== Are you new here? ==
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies.
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.
* 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").

We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.

== Products ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org]
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons]
|-
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}

== Topics ==
{| class="wikitable"
|-
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]]
|| [[Hit picking party]]
|-
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]]
|-
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] ||  
|}

== Other topics ==
{| class="wikitable"
|-
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]]
|-
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]]
|-
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]]
|}

== Organizational ==
{| class="wikitable"
|-
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]]
|-
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]]
|}

Still haven't found what you're looking for? Try the search bar top right to see if that works...

= Outages and Support =
* We communicate about outages and updates via [https://twitter.com/chem4biology X].
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server]
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
* More about ways to [[feedback | communicate with us]].
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free.

= Policies, Privacy and all that =
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]].

[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]

Main Page

2025-02-21T18:13:42Z

Sstrizhov: removed contribute text as people will be contributing anyway if they wish to, and there's no need to have this on the landing page

<div id="mainpage"></div>__NOTOC__
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". This wiki serves several [[:Category:Roles | constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic.

If you are a new member of a lab, please follow the [[Welcome group members | following guide]].

=== Relevant Links ===
* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]
* [[:Category:News | News]]
* [https://x.com/chem4biology/ Outages and Updates]
* [https://discord.gg/4MpD6UF5AN Chat on Discord]

== Are you new here? ==
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies.
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.
* 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").

We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.

== Products ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org]
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons]
|-
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}

== Topics ==
{| class="wikitable"
|-
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]]
|| [[Hit picking party]]
|-
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]]
|-
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] ||  
|}

== Other topics ==
{| class="wikitable"
|-
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]]
|-
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]]
|-
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]]
|}

== Organizational ==
{| class="wikitable"
|-
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]]
|-
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]]
|}

Still haven't found what you're looking for? Try the search bar top right to see if that works...

= Outages and Support =
* We communicate about outages and updates via [https://twitter.com/chem4biology X].
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server]
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
* More about ways to [[feedback | communicate with us]].
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free.

= Policies, Privacy and all that =
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]].

[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]

Main Page

2025-02-21T18:10:38Z

Sstrizhov: some page visual updates

<div id="mainpage"></div>__NOTOC__
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". To contribute, login and [[contribute | edit to help us improve]] (please!). This wiki serves several [[:Category:Roles | constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic.

If you are a new member of a lab, please follow the [[Welcome group members | following guide]].

=== Relevant Links ===
* [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback Form]
* [[:Category:News | News]]
* [https://x.com/chem4biology/ Outages and Updates]
* [https://discord.gg/4MpD6UF5AN Chat on Discord]

== Are you new here? ==
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies.
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.
* 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").

We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.

== Products ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org]
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons]
|-
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}

== Topics ==
{| class="wikitable"
|-
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]]
|| [[Hit picking party]]
|-
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]]
|-
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] ||  
|}

== Other topics ==
{| class="wikitable"
|-
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]]
|-
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]]
|-
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]]
|}

== Organizational ==
{| class="wikitable"
|-
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]]
|-
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]]
|}

Still haven't found what you're looking for? Try the search bar top right to see if that works...

= Outages and Support =
* We communicate about outages and updates via [https://twitter.com/chem4biology X].
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server]
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
* More about ways to [[feedback | communicate with us]].
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free.

= Policies, Privacy and all that =
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]].

[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]

Main Page

2025-02-21T18:07:31Z

Sstrizhov: oops typo fix

<div id="mainpage"></div>__NOTOC__
Welcome to DISI (Disi Is Still Incomplete, "dizzy"), the wiki of the [[Shoichet Lab]] and [[Irwin Lab]] at [[UCSF]]. This wiki aims to document our software tools, databases, protocols and resources related to computational ligand discovery, molecular docking and systems pharmacology as hosted at the domain "docking.org". To contribute, login and [[contribute | edit to help us improve]] (please!). This wiki serves several [[:Category:Roles | constituencies]]. Many pages are designed for specific audiences and may not make much sense to a reader who is not the target demographic. [https://forms.gle/LZV1FCmLWxUWznVi9 Feedback form]. [[:Category:News | News]] [https://x.com/chem4biology/ Outages and updates]. [https://discord.gg/4MpD6UF5AN chat on discord]

If you are a new member of a lab, please follow the [[Welcome group members | following guide]].

== Are you new here? ==
wiki.docking.org documents the efforts in the Shoichet and Irwin labs at UCSF to provide tools and databases for ligand (drug) discovery to investigators worldwide, both in academia and in companies. We use three core technologies.
* 1) '''Molecular docking screens''' take a library of compounds that are easy to acquire for experimental testing. Investigators who use molecular docking often find completely novel molecules that modulate biology (see [ https://bkslab.org/publications]).
* 2) '''Analog-by-catalog''' works on the molecular similarity principle. Once a compound is found to modulate a protein target, a logical and efficient next step is to test close analogs for higher (or lower) activity. By exploring the chemical space around an active, compounds can be "optimized" for both activity as well as other molecular properties.
* 3) '''Target prediction'''. Given a molecule, our program SEA can predict possible molecular targets based on its resemblance of known actives. In this way, the activity of a compound with an unknown molecular explanation (e.g. phenotypic hits) can be attributed to a particular molecular target ("mechanism of action").

We also curate the databases underlying these tools. This website can be a little cryptic as it is designed for specific, technical audiences. Still we hope you find it interesting and useful. If you have any questions, please write to chemistry 4 biology at gmail dot com, or use one of the many other communication channels we support.

== Products ==
{| class="wikitable"
|-
! Main article !! Description !! Notes/Links
|-
| [[:Category:DOCK |DOCK]] || Our molecular docking software || There are two main branches. The latest are [[DOCK 3.8]] and [[DOCK 6]].11 [https://dock.docking.org dock.docking.org]
|-
| [[:Category:ZINC|ZINC]] || Commercially available compounds || There are two databases [https://zinc20.docking.org zinc20] [https://cartblanche22.docking.org zinc22]
|-
| [[SEA]] || Similarity Ensemble Approach || Drug repurposing, target identification, phenotypic screening. [https://sea.bkslab.org/ sea.bkslab.org]
|-
| [[DUDE Family]] || Benchmarks for docking|| [https://dude.docking.org/generate dude.docking.org/generate]
|-
| [[TLDR]] ||TLDR is a Ligand Discovery Resource || [https://tldr.docking.org TLDR]
|-
| [[Chemistry Commons]] ||Chemistry Commons || [https://commons.docking.org Chemistry Commons]
|-
| [[DOCK Blaster]] || A public access service for docking screens || [https://blaster.docking.org blaster.docking.org]
|}

== Topics ==
{| class="wikitable"
|-
| [[:Category:Databases | Databases]] || [[:Category:Docking|Molecular Docking]] || [[:Category:Aggregation| Colloidal aggregation]]
|| [[Hit picking party]]
|-
| [[:Category:Systems pharmacology | Systems pharmacology]] || [[:Category:Covalent | Covalent docking]] || [[Chemical Space]] || [[Decoys]]
|-
| [[Fragment Docking]] || [[Excipients]] || [[:Category:Model systems | Model systems ]] ||  
|}

== Other topics ==
{| class="wikitable"
|-
| [[Welcome group members | Lab members with ssh]] || [[Welcome web user | Non members without ssh ]] || [[Assaying Compound Activity]]
|-
| [[Run on our servers]] || [[Run on your servers]] || [[Set up a lab]]
|-
| [[:Category:API | programmatic access (API) ]] || [[:Category:Software|Software ]] || [[Aggregator advisor]]
|}

== Organizational ==
{| class="wikitable"
|-
| [[:Category:Topic | Topics]] || [[:Category:Roles | Who are you?]] || [[:Category:Idioms | Idioms]]
|| [[:Category:Article type | Article type]] || [[:Category:Attributes |Attributes]] || [[:Category:Policy | Policies]]
|-
| [[Special:Categories| Categories]] || [[:Category:Tutorials | Tutorials ]]
|| [[:Category:Problems | Problems]] || [[:Category:FAQ|FAQ]] || [[:Category:Manual | Manuals ]] || [[:Category:Jargon | Jargon]]
|}

Still haven't found what you're looking for? Try the search bar top right to see if that works...

= Outages and Support =
* We communicate about outages and updates via [https://twitter.com/chem4biology X].
* We have open conversations among ourselves and with users on our discord server. [https://discord.gg/4MpD6UF5AN discord server]
* If our servers appear down or broken and you think we might not have noticed, and we don't reply to you, please tell us via jjiteam at googlegroups dot com or my text/voice to +1 (415) 937-1461
* [https://forms.gle/LZV1FCmLWxUWznVi9 Tell us how we are doing].
* More about ways to [[feedback | communicate with us]].
* [[Weekly office hours]]. 11 am PT is the 'daily' office hours on discord, if we are free.

= Policies, Privacy and all that =
We aim to keep confidential information such as passwords secure, but we offer no guarantees. You must use these services at your own risk. See our [[DISI:Privacy_policy|privacy policy]].

[[Category:FAQ]]
[[Category:Public]]
[[Category:Organization]]
[[Category:Navigation]]