maag - User contributions [en]

BikingDTU

2024-03-20T13:19:03Z

WikiSysop: Created page with " Here are some interesting biking destinations: Visit the troll in the forest close to Allerød: https://goo.gl/maps/uv3f76k1RwAahNnV8 The Dyrehave to see some deers up close: https://goo.gl/maps/SWforuzvrDsSshAC6 The Vedbæk harbor: https://goo.gl/maps/XnXSCNJSLrxBUoHe6 Amusement park Bakken: https://goo.gl/maps/W5cGcaGnTLGYPPiE9 The open-air museum, Frilandsmuseet: https://goo.gl/maps/SvQzodcDjHo5Sgd97"

Here are some interesting biking destinations:

Visit the troll in the forest close to Allerød:
https://goo.gl/maps/uv3f76k1RwAahNnV8

The Dyrehave to see some deers up close:
https://goo.gl/maps/SWforuzvrDsSshAC6

The Vedbæk harbor:
https://goo.gl/maps/XnXSCNJSLrxBUoHe6

Amusement park Bakken:
https://goo.gl/maps/W5cGcaGnTLGYPPiE9

The open-air museum, Frilandsmuseet:
https://goo.gl/maps/SvQzodcDjHo5Sgd97

BookingMeeting

2024-03-20T13:18:41Z

WikiSysop: Created page with "How to book a room? Go to your Outlook calendar: https://mail.win.dtu.dk/owa/#path=/calendar/view/Month # Click on the date where you want to create the event # Click "more details" # edit the time and make sure the day is correct # you should see an empty field that says "add location or room", click on it # then you can select the room you want from a list, you can use: "DTU open meeting rooms" for first floor of 202 "DTU Lifesciences bios meeting rooms" for upper..."

How to book a room?

Go to your Outlook calendar:

https://mail.win.dtu.dk/owa/#path=/calendar/view/Month

# Click on the date where you want to create the event
# Click "more details"
# edit the time and make sure the day is correct
# you should see an empty field that says "add location or room", click on it
# then you can select the room you want from a list, you can use:

"DTU open meeting rooms" for first floor of 202

"DTU Lifesciences bios meeting rooms" for upper floors of 202 and 204.

Healthtech cluster

2024-03-20T13:18:15Z

WikiSysop: Created page with "== Getting an account == Contact Gabriel Renaud and we will contact Peter Wad Sackett. == First time login == * Do you have a DTU account? If not contact Gabriel. * Have you changed DTU password after August 2021? If not, change it at password.dtu.dk <!-- * Download either [https://play.google.com/store/apps/details?id=com.azure.authenticator&hl=en&gl=US Microsoft Authenticator] or [https://play.google.com/store/apps/details?id=com.google.android.apps.authenticator2&..."

== Getting an account ==

Contact Gabriel Renaud and we will contact Peter Wad Sackett.

== First time login ==

* Do you have a DTU account? If not contact Gabriel.
* Have you changed DTU password after August 2021? If not, change it at password.dtu.dk

* If you can log in to DTU webmail [https://mail.dtu.dk https://mail.dtu.dk], your credentials should be in order.
* If you can not login in to DTU webmail, you should set up the MFA (2-factor authentication). We refer to DTU general instructions on how to do that.
* At this stage try to login using your DTU username and password:
<pre>
ssh -XC <username>@login.healthtech.dtu.dk
Example: ssh -XC gabre@login.healthtech.dtu.dk
</pre>
* You will be prompted for the password (you can not see the chars you type), and the MFA code.

* If you can not login at this stage, using your DTU username, password and MFA, then you are probably not enrolled into Microsoft Azure. [https://account.activedirectory.windowsazure.com/proofup.aspx?proofup=1 Enroll here]. Use your DTU email as username. You will be taken to the DTU login procedure for verification of your identity.<br>Efter the enrollment, try to login again.
* Logout again using Ctrl D or typing "logout".

== Subsequent logins ==

* Login using:
<pre>
ssh -XC <username>@login.healthtech.dtu.dk
</pre>
* Enter your DTU password and the MFA password when prompted

* You should see:
<pre>
<username>@login ~$
</pre>
'''This is the login node, do not run anything there.
'''
* Then select a node from 01 to 14:
<pre>
ssh -XC <username>@nodeX
</pre>
where X is 01, 02, 03, ..., 14
* if this is your first time logging in, '''read''' the:
<pre>
/home/README.txt
</pre>
very carefully WHEN on a node. It will tell you where the different directories are.
* Check if the Node is busy using:
<pre>
htop
</pre>

You will see the CPUs on top and the memory.

== Nodes ==

{| class="wikitable"
! style="text-align:left;"| NodeID
! CPUs
! GHz (7z)
! | MIPS (7z)
! Memory (kb)
|-
| | node01
| | 24
| | 2.67GHz
| 3197
| | 64,304
|-
| | node02
| | 16
| | 2.40GHz
| 2898
| | 64,402
|-
| | node03
| | 24
| | 3.07GHz
| 3713
| | 96,656
|-
| | node04
| | 24
| | 2.93GHz
| 3551
| | 193,424
|-
| | node05
| | 24
| | 3.33GHz
| 3773
| | 193,424
|-
| | node06
| | 24
| | 2.40GHz
| 3017
| | 64,400
|-
| | node07
| | 64
| | 2.70GHz
| 3463
| | 515,942
|-
| | node08
| | 20
| | 2.30GHz
| 3456
| | 128,796
|-
| | node09
| | 16
| | 2.53GHz
| 2991
| | 120,853
|-
| | node10
| | 16
| | 2.53GHz
| 2985
| | 120,853
|-
| | node11
| 40
| | 2.60GHz
| 3872
| | 257,847
|-
| | node12
| 16
| | 2.80GHz
| 3458
| | 24,081
|-
| | node13
| 16
| | 2.53GHz
| 3036
| | 24,081
|-
| | node14
| 16
| | 2.43GHz
| 3002
| | 128,913
|-
| | compute01
| 128
| | 3.53GHz
| | 3671
| | 1,056,315

|}

== Running things in parallel ==

There is no queuing system on the cluster. But that can be simulated using parallel. First, write a file with the commands, let's call it "list_cmds". We need full paths, no relative paths.
Then pick a host server to launch the commands from, I pick node10 because it is the slowest (then I keep the faster nodes for
computations): you write:

cat list_cmds | parallel --slf list_serv_1_14minus10

And the file: list_serv_1_14minus10 has:
node01
node02
node03
node04
node05
node06
node07
node08
node09
node11
node12
node13
node14

== General considerations ==

You can ssh to the login node and, once on the login node to other nodes without 2 factor or a password using ssh keys. To set up the ssh keys and not have to type your password+2FA, find instructions here: [[Sshnopassword]].

'''Do not forget''' to nice -19 your commands.

HowtoreachGabrielsoffice

2024-03-20T13:17:45Z

WikiSysop: Created page with "== How to reach Gabriel's office == # head to [https://goo.gl/maps/RtFktTm8QkmvFpqX8 DTU building 202] # either take the stairs or elevator two floors up # follow the arrows to building 204 # cross the little "sky bridge" # when arriving in 204, make a turn right in the hallway # I am in office 249A [https://youtu.be/eeFdU-2e4xQ Watch Youtube video here]"

== How to reach Gabriel's office ==

# head to [https://goo.gl/maps/RtFktTm8QkmvFpqX8 DTU building 202]
# either take the stairs or elevator two floors up
# follow the arrows to building 204
# cross the little "sky bridge"
# when arriving in 204, make a turn right in the hallway
# I am in office 249A

[https://youtu.be/eeFdU-2e4xQ Watch Youtube video here]

Group meetings

2024-03-20T13:14:47Z

WikiSysop: Created page with " {| class="wikitable" |+ |- ! Date !! Room !! Presenter !! Topic |- | Feburary 14th 2024 || 202-R8209 || Karolina Tudelska || marthe |- | Feburary 14th 2024 || 202-R8209 || Josh Rubin || SAFARI |- | Feburary 7th 2024 || 202-R8209 || Adresya Azhakath || thesis work |- | January 31th 2024 || 202-R8209 || Gabriel Renaud || What will a reviewer look for in a paper? |- | November 29th 2023 || 202-R8209 || Nicola Vogel || soibean |- | June 14th 2023 || 202-R8209 || J..."

{| class="wikitable"
|+
|-
! Date !! Room !! Presenter !! Topic
|-
| Feburary 14th 2024 || 202-R8209 || Karolina Tudelska || marthe
|-
| Feburary 14th 2024 || 202-R8209 || Josh Rubin || SAFARI
|-
| Feburary 7th 2024 || 202-R8209 || Adresya Azhakath || thesis work
|-
| January 31th 2024 || 202-R8209 || Gabriel Renaud || What will a reviewer look for in a paper?
|-
| November 29th 2023 || 202-R8209 || Nicola Vogel || soibean
|-
| June 14th 2023 || 202-R8209 || Josh Rubin || Mashmap
|-
| June 7th 2023 || 202-R8209 || no one || cancelled
|-
| May 31th 2023 || 202-R8209 || Jan van Waaij || project update
|-
| May 24th 2023 || 202-R8209 || Louis Kraft || project update
|-
| May 17th 2023 || 202-R8209 || Nicola Vogel || future project
|-
| April 25th 2023 || 202-R8209 || Gabriel Renaud || various papers
|-
| March 22nd 2023 || 202-R8209 || Louis Kraft || rymer
|-
| March 15th 2023 || 202-R8209 || Jan van Waaij || practice floor talk
|-
| March 8th 2023 || 202-R8209 || Gabriel Renaud || Extraordinary selection on the human X
chromosome associated with archaic admixture
|-
| March 1st 2023 || 202-R8209 || Jan van Waaij || practice floor talk
|-
| February 22ndth 2023 || 202-R8209 || Nicola Vogel || ?
|-
| February 15th 2023 || 202-R8209 || Angela Miranda Segura || marthe
|-
| February 8th 2023 || 202-R8209 || Josh Rubin || TrailMix
|-
| February 1st 2023 || 202-R8209 || Gabriel Renaud || conferences in 2023
|-
| October 12th 2022 || 202-R8209 || Louis Kraft || cool paper
|-
| October 5th 2022 || 202-R8209 || Angela Miranda Segura || Master's project
|-
| September 28th 2022 || 202-R8209 || Josh Rubin || Summary of EESHuman
|-
| September 21th 2022 || 202-R8209 || Josh Rubin || Summary of EESHuman
|-
| September 14th 2022 || 202-R8209 || Gabriel Renaud || Hunter-gatherer admixture facilitated natural
2 selection in Neolithic European farmers (https://www.biorxiv.org/content/10.1101/2022.09.05.506481v1.full.pdf)
|-
| September 7th 2022 || 202-R8209 || Gabriel Renaud || canceled
|-
| August 31th 2022 || 202-R8209 || Jan van Waaij || Racimo model for genotypes.
|-
| August 24th 2022 || 202-R8209 || Gabriel Renaud || interesting recent papers
|-
| August 17th 2022 || 202-R8209 || Louis Kraft || PhD project
|-
| June 29th 2022 || 202-R8209 || Isabel Díaz-Pinés Cort || Master's project
|-
| May 25th 2022 || 202-R8209 || TBD || TBD
|-
| May 18th 2022 || 202-R8209 || Vanessa Carina Bieker || How herbarium specimens help us understand invasion processes: the case of Ambrosia artemisifoliia (common ragweed)
|-
| May 11th 2022 || 202-R8209 || Trine Zachariasen || New project
|-
| May 4th 2022 || 202-R8209 || Isabel Díaz-Pinés Cort || Master's project
|-
| April 27th 2022 || 202-R8209 || Paul Jeremy Simon || Master's project
|-
| April 20th 2022 || 202-R8209 || Gabriel Renaud|| A unified genealogy of modern and ancient genomes
https://www.science.org/doi/10.1126/science.abi8264 https://www.youtube.com/watch?v=xqy2-m080jY
|-
| April 13th 2022 || 202-R8209 || TBD || TBD
|-
| April 6th 2022 || 202-R8209 || Louis Kraft || Master's thesis presentation
|-
| March 30th 2022 || 202-R8209 || Sofus Wiisbye || Master's project
|-
| March 23rd 2022 || 202-R8209 || Josh Rubin || PhD project
|-
| March 16th 2022 || 202-R8209 || Sofus Wiisbye || Master's project
|-
| March 9th 2022 || none || canceled || canceled
|-
| March 2nd 2022 || 202-R8209 || Nicola Vogel || PhD project
|-
| Feb 23 2022 || none || canceled || canceled
|-
| Feb 16 2022 || 202-R8209 || Trine Zachariasen || Profiling of metagenomics data by the use of signature genes
|-
| Feb 9 2022 || 202-R8209 || Alexandra Balicki || master's project
|-
| January 26th 2022 || 202-R8209 || Gabriel Renaud || review of bioinformatics paper about contamination.
|-
| October 26th 2021 || 202-R8209 || Nicola ||
|-
| October 19th 2021 || 202-R8209 || Josh ||
|-
| October 12th 2021 || 202-R8209 || Gabriel || paper: Patterns of damage in genomic DNA sequences from a Neandertal Adrian W. Briggs, Udo Stenzel, Philip L. F. Johnson, Richard E. Green, Janet Kelso, Kay Prüfer, Matthias Meyer, Johannes Krause, Michael T. Ronan, Michael Lachmann, Svante Pääbo Proceedings of the National Academy of Sciences Sep 2007, 104 (37) 14616-14621; https://www.pnas.org/content/pnas/104/37/14616.full.pdf
|-
|}

Main Page

2024-03-20T13:14:17Z

WikiSysop:

<strong>Wiki for the Modern and Ancient Genomes group.</strong>

== Various pages: ==

[[Group_meetings|Schedules for group meetings]]

[[HowtoreachGabrielsoffice|How to reach Gabriel's office ]]

[[Healthtech_cluster|Information on the Healthtech Cluster]]

[[BookingMeeting|How to book meeting rooms]]

[[BikingDTU|Good biking destinations close to DTU]]

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