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#nanopub — Public Fediverse posts

Live and recent posts from across the Fediverse tagged #nanopub, aggregated by home.social.

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  1. Today-I-have-done:

    - first login to the cluster I should work and teach on
    - installed #Snakemake and the #SLURM plugin, both using #pixi Noticed that I need to amend the docs for this.
    - installed the #Nanopub reporter plugin, too.
    - merged a couple of dependency PRs (those are auto-generated) for the Nanopub plugin.
    - Finished the onboarding part for the course which I intend to give. There still is no release.
    - saw a notice from the Snakemake announcement bot account (fediscience.org/@snakemake/117 ) and remembered, that I wanted to get rid of the serif font. Needs some tinkering. So, not this fix will not be there too soon, I'm afraid. @johanneskoester this is not forgotten!

    Something, I have not done, but Johannes, is to set up the Fediwall for Snakemake (see snakemake.github.io/fediwall/ ) - for which I need to include the announcement robot, too.

    (This series of posts is not a thread of posts - otherwise all Snakemake related stuff would not show up on the Fediwall.)

    3/n

  2. Today-I-have-done:

    - first login to the cluster I should work and teach on
    - installed #Snakemake and the #SLURM plugin, both using #pixi Noticed that I need to amend the docs for this.
    - installed the #Nanopub reporter plugin, too.
    - merged a couple of dependency PRs (those are auto-generated) for the Nanopub plugin.
    - Finished the onboarding part for the course which I intend to give. There still is no release.
    - saw a notice from the Snakemake announcement bot account (fediscience.org/@snakemake/117 ) and remembered, that I wanted to get rid of the serif font. Needs some tinkering. So, not this fix will not be there too soon, I'm afraid. @johanneskoester this is not forgotten!

    Something, I have not done, but Johannes, is to set up the Fediwall for Snakemake (see snakemake.github.io/fediwall/ ) - for which I need to include the announcement robot, too.

    (This series of posts is not a thread of posts - otherwise all Snakemake related stuff would not show up on the Fediwall.)

    3/n

  3. Today-I-have-done:

    - first login to the cluster I should work and teach on
    - installed #Snakemake and the #SLURM plugin, both using #pixi Noticed that I need to amend the docs for this.
    - installed the #Nanopub reporter plugin, too.
    - merged a couple of dependency PRs (those are auto-generated) for the Nanopub plugin.
    - Finished the onboarding part for the course which I intend to give. There still is no release.
    - saw a notice from the Snakemake announcement bot account (fediscience.org/@snakemake/117 ) and remembered, that I wanted to get rid of the serif font. Needs some tinkering. So, not this fix will not be there too soon, I'm afraid. @johanneskoester this is not forgotten!

    Something, I have not done, but Johannes, is to set up the Fediwall for Snakemake (see snakemake.github.io/fediwall/ ) - for which I need to include the announcement robot, too.

    (This series of posts is not a thread of posts - otherwise all Snakemake related stuff would not show up on the Fediwall.)

    3/n

  4. Today-I-have-done:

    - first login to the cluster I should work and teach on
    - installed #Snakemake and the #SLURM plugin, both using #pixi Noticed that I need to amend the docs for this.
    - installed the #Nanopub reporter plugin, too.
    - merged a couple of dependency PRs (those are auto-generated) for the Nanopub plugin.
    - Finished the onboarding part for the course which I intend to give. There still is no release.
    - saw a notice from the Snakemake announcement bot account (fediscience.org/@snakemake/117 ) and remembered, that I wanted to get rid of the serif font. Needs some tinkering. So, not this fix will not be there too soon, I'm afraid. @johanneskoester this is not forgotten!

    Something, I have not done, but Johannes, is to set up the Fediwall for Snakemake (see snakemake.github.io/fediwall/ ) - for which I need to include the announcement robot, too.

    (This series of posts is not a thread of posts - otherwise all Snakemake related stuff would not show up on the Fediwall.)

    3/n

  5. Today-I-have-done:

    - first login to the cluster I should work and teach on
    - installed #Snakemake and the #SLURM plugin, both using #pixi Noticed that I need to amend the docs for this.
    - installed the #Nanopub reporter plugin, too.
    - merged a couple of dependency PRs (those are auto-generated) for the Nanopub plugin.
    - Finished the onboarding part for the course which I intend to give. There still is no release.
    - saw a notice from the Snakemake announcement bot account (fediscience.org/@snakemake/117 ) and remembered, that I wanted to get rid of the serif font. Needs some tinkering. So, not this fix will not be there too soon, I'm afraid. @johanneskoester this is not forgotten!

    Something, I have not done, but Johannes, is to set up the Fediwall for Snakemake (see snakemake.github.io/fediwall/ ) - for which I need to include the announcement robot, too.

    (This series of posts is not a thread of posts - otherwise all Snakemake related stuff would not show up on the Fediwall.)

    3/n

  6. As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement.

    Next Monday I will start on a new position. And I have to commute. Possibly no time to take a break for posting on social media during working hours. Hence, the idea of posting little partially research-related summary posts is appealing to me.

    Let me start:
    - I tinkered with a #Fediwall for #Snakemake (cmeesters.github.io/Snakemake-). It will not be the final FediWall page as this is merely an experiment. But my idea is that as science communicators in the Fediverse we have to provide information proactively and not wait for demand to magically develop. So, this is a first step. (We cannot expect everyone to have a fable for social media - this will work for anyone without an account, too.)
    - I did a few updates to the #HPC teaching material for Snakemake. We had a little "alliance" of like-minded people developing this material. A few drop-outs and a pretty LaTeX-oriented and obfuscated development environment and it was basically me. But I know there is some interest and I hope to be able to revive this group. Also, essentially new courses are on the horizon already.
    - Last not least, some work on the teaching material for Snakemake #nanopub reporter plugin.

    There are no releases, yet.

    1/n

  7. As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement.

    Next Monday I will start on a new position. And I have to commute. Possibly no time to take a break for posting on social media during working hours. Hence, the idea of posting little partially research-related summary posts is appealing to me.

    Let me start:
    - I tinkered with a #Fediwall for #Snakemake (cmeesters.github.io/Snakemake-). It will not be the final FediWall page as this is merely an experiment. But my idea is that as science communicators in the Fediverse we have to provide information proactively and not wait for demand to magically develop. So, this is a first step. (We cannot expect everyone to have a fable for social media - this will work for anyone without an account, too.)
    - I did a few updates to the #HPC teaching material for Snakemake. We had a little "alliance" of like-minded people developing this material. A few drop-outs and a pretty LaTeX-oriented and obfuscated development environment and it was basically me. But I know there is some interest and I hope to be able to revive this group. Also, essentially new courses are on the horizon already.
    - Last not least, some work on the teaching material for Snakemake #nanopub reporter plugin.

    There are no releases, yet.

    1/n

  8. As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement.

    Next Monday I will start on a new position. And I have to commute. Possibly no time to take a break for posting on social media during working hours. Hence, the idea of posting little partially research-related summary posts is appealing to me.

    Let me start:
    - I tinkered with a #Fediwall for #Snakemake (cmeesters.github.io/Snakemake-). It will not be the final FediWall page as this is merely an experiment. But my idea is that as science communicators in the Fediverse we have to provide information proactively and not wait for demand to magically develop. So, this is a first step. (We cannot expect everyone to have a fable for social media - this will work for anyone without an account, too.)
    - I did a few updates to the #HPC teaching material for Snakemake. We had a little "alliance" of like-minded people developing this material. A few drop-outs and a pretty LaTeX-oriented and obfuscated development environment and it was basically me. But I know there is some interest and I hope to be able to revive this group. Also, essentially new courses are on the horizon already.
    - Last not least, some work on the teaching material for Snakemake #nanopub reporter plugin.

    There are no releases, yet.

    1/n

  9. As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement.

    Next Monday I will start on a new position. And I have to commute. Possibly no time to take a break for posting on social media during working hours. Hence, the idea of posting little partially research-related summary posts is appealing to me.

    Let me start:
    - I tinkered with a #Fediwall for #Snakemake (cmeesters.github.io/Snakemake-). It will not be the final FediWall page as this is merely an experiment. But my idea is that as science communicators in the Fediverse we have to provide information proactively and not wait for demand to magically develop. So, this is a first step. (We cannot expect everyone to have a fable for social media - this will work for anyone without an account, too.)
    - I did a few updates to the #HPC teaching material for Snakemake. We had a little "alliance" of like-minded people developing this material. A few drop-outs and a pretty LaTeX-oriented and obfuscated development environment and it was basically me. But I know there is some interest and I hope to be able to revive this group. Also, essentially new courses are on the horizon already.
    - Last not least, some work on the teaching material for Snakemake #nanopub reporter plugin.

    There are no releases, yet.

    1/n

  10. As of today, I will be starting a today-I-have-done series. Already tried before. Possibly with breaks, as I will not always find the time to post. Sometimes, I might sprinkle in a blog post or event announcement.

    Next Monday I will start on a new position. And I have to commute. Possibly no time to take a break for posting on social media during working hours. Hence, the idea of posting little partially research-related summary posts is appealing to me.

    Let me start:
    - I tinkered with a #Fediwall for #Snakemake (cmeesters.github.io/Snakemake-). It will not be the final FediWall page as this is merely an experiment. But my idea is that as science communicators in the Fediverse we have to provide information proactively and not wait for demand to magically develop. So, this is a first step. (We cannot expect everyone to have a fable for social media - this will work for anyone without an account, too.)
    - I did a few updates to the #HPC teaching material for Snakemake. We had a little "alliance" of like-minded people developing this material. A few drop-outs and a pretty LaTeX-oriented and obfuscated development environment and it was basically me. But I know there is some interest and I hope to be able to revive this group. Also, essentially new courses are on the horizon already.
    - Last not least, some work on the teaching material for Snakemake #nanopub reporter plugin.

    There are no releases, yet.

    1/n

  11. @saranjeet this is one use case for our onboarding slide set 😉 . Hope, you found a #nanopub use case, too. Perhaps, next time, I will propose a SparQL 101 set 🤔

  12. @saranjeet this is one use case for our onboarding slide set 😉 . Hope, you found a #nanopub use case, too. Perhaps, next time, I will propose a SparQL 101 set 🤔

  13. @saranjeet this is one use case for our onboarding slide set 😉 . Hope, you found a #nanopub use case, too. Perhaps, next time, I will propose a SparQL 101 set 🤔

  14. @saranjeet this is one use case for our onboarding slide set 😉 . Hope, you found a #nanopub use case, too. Perhaps, next time, I will propose a SparQL 101 set 🤔

  15. @saranjeet this is one use case for our onboarding slide set 😉 . Hope, you found a #nanopub use case, too. Perhaps, next time, I will propose a SparQL 101 set 🤔

  16. @egonw @cthoyt @nanopub

    In fact, for similar associations templates exist (e.g. purl.org/np/RA2oeXmfW1JZIIp6Wv ). Haven't seen snp-db specific references, though.

    @yokofakun congrats for sucessfully onboarding to #nanopub ;-)

  17. @egonw @cthoyt @nanopub

    In fact, for similar associations templates exist (e.g. purl.org/np/RA2oeXmfW1JZIIp6Wv ). Haven't seen snp-db specific references, though.

    @yokofakun congrats for sucessfully onboarding to #nanopub ;-)

  18. @egonw @cthoyt @nanopub

    In fact, for similar associations templates exist (e.g. purl.org/np/RA2oeXmfW1JZIIp6Wv ). Haven't seen snp-db specific references, though.

    @yokofakun congrats for sucessfully onboarding to #nanopub ;-)

  19. @egonw @cthoyt @nanopub

    In fact, for similar associations templates exist (e.g. purl.org/np/RA2oeXmfW1JZIIp6Wv ). Haven't seen snp-db specific references, though.

    @yokofakun congrats for sucessfully onboarding to #nanopub ;-)

  20. @egonw @cthoyt @nanopub

    In fact, for similar associations templates exist (e.g. purl.org/np/RA2oeXmfW1JZIIp6Wv ). Haven't seen snp-db specific references, though.

    @yokofakun congrats for sucessfully onboarding to #nanopub ;-)

  21. Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

    Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": w3id.org/np/RAxi5mJwS-F0iSUJ73

    Nice read!

  22. Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

    Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": w3id.org/np/RAxi5mJwS-F0iSUJ73

    Nice read!

  23. Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

    Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": w3id.org/np/RAxi5mJwS-F0iSUJ73

    Nice read!

  24. Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

    Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": w3id.org/np/RAxi5mJwS-F0iSUJ73

    Nice read!

  25. Just discovered that the new "Paper I have read" #nanopub template has a label field. This will be quite a motivation for me to register more for some time to SparQL in the future.

    Could not resist registering the #OSPARK output by @saranjeet and others about "Managing Outreach on Open Research Material to Heterogeneous Groups": w3id.org/np/RAxi5mJwS-F0iSUJ73

    Nice read!

  26. RE: mas.to/@nanopub/11661902643127

    A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

    Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to fediscience.org/@snakemake/116 - oh, and I just realized a typo in the announcement bot message 😉

  27. RE: mas.to/@nanopub/11661902643127

    A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

    Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to fediscience.org/@snakemake/116 - oh, and I just realized a typo in the announcement bot message 😉

  28. RE: mas.to/@nanopub/11661902643127

    A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

    Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to fediscience.org/@snakemake/116 - oh, and I just realized a typo in the announcement bot message 😉

  29. RE: mas.to/@nanopub/11661902643127

    A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

    Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to fediscience.org/@snakemake/116 - oh, and I just realized a typo in the announcement bot message 😉

  30. RE: mas.to/@nanopub/11661902643127

    A presentation about #Snakemake and software provenance with #nanopub by Yours Truthfully.

    Of interest for those in the Snakemake workflow management system and citing workflow metadata in academic journals. Related to fediscience.org/@snakemake/116 - oh, and I just realized a typo in the announcement bot message 😉

  31. Today:

    - written a blurb for my presentation at the upcoming #nanopub session
    - release the #SLURM executor plugin for #Snakemake v2.7.0 - see fediscience.org/@snakemake/116
    - tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
    - futile further debugging attempts. In the end it worked. Might result in a new release next week.

    #academicchatter

  32. Today:

    - written a blurb for my presentation at the upcoming #nanopub session
    - release the #SLURM executor plugin for #Snakemake v2.7.0 - see fediscience.org/@snakemake/116
    - tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
    - futile further debugging attempts. In the end it worked. Might result in a new release next week.

    #academicchatter

  33. Today:

    - written a blurb for my presentation at the upcoming #nanopub session
    - release the #SLURM executor plugin for #Snakemake v2.7.0 - see fediscience.org/@snakemake/116
    - tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
    - futile further debugging attempts. In the end it worked. Might result in a new release next week.

    #academicchatter

  34. Today:

    - written a blurb for my presentation at the upcoming #nanopub session
    - release the #SLURM executor plugin for #Snakemake v2.7.0 - see fediscience.org/@snakemake/116
    - tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
    - futile further debugging attempts. In the end it worked. Might result in a new release next week.

    #academicchatter

  35. Today:

    - written a blurb for my presentation at the upcoming #nanopub session
    - release the #SLURM executor plugin for #Snakemake v2.7.0 - see fediscience.org/@snakemake/116
    - tried to mitigate the issue that TMOUT on an HPC login brings: sending SIGHUB to all detached multiplexers (so far no remedy and I tried a lot(!), don't send me tips).
    - futile further debugging attempts. In the end it worked. Might result in a new release next week.

    #academicchatter

  36. ... and two more, to get

    - Snakemake workflow registrations: w3id.org/np/RApMWbZ0ixGj88tPB4
    - or Snakemake report registrations: w3id.org/np/RA8rPcBcreaZF01eA6

    just to make a start. Pretty crude, but a start towards better software provenance.

    #nanopub #Snakemake

  37. ... and two more, to get

    - Snakemake workflow registrations: w3id.org/np/RApMWbZ0ixGj88tPB4
    - or Snakemake report registrations: w3id.org/np/RA8rPcBcreaZF01eA6

    just to make a start. Pretty crude, but a start towards better software provenance.

    #nanopub #Snakemake

  38. ... and two more, to get

    - Snakemake workflow registrations: w3id.org/np/RApMWbZ0ixGj88tPB4
    - or Snakemake report registrations: w3id.org/np/RA8rPcBcreaZF01eA6

    just to make a start. Pretty crude, but a start towards better software provenance.

    #nanopub #Snakemake

  39. ... and two more, to get

    - Snakemake workflow registrations: w3id.org/np/RApMWbZ0ixGj88tPB4
    - or Snakemake report registrations: w3id.org/np/RA8rPcBcreaZF01eA6

    just to make a start. Pretty crude, but a start towards better software provenance.

    #nanopub #Snakemake

  40. ... and two more, to get

    - Snakemake workflow registrations: w3id.org/np/RApMWbZ0ixGj88tPB4
    - or Snakemake report registrations: w3id.org/np/RA8rPcBcreaZF01eA6

    just to make a start. Pretty crude, but a start towards better software provenance.

    #nanopub #Snakemake

  41. Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: w3id.org/np/RAzeQbv1gXqKIuLic4

    Not yet sophisticated, but I am starting to like #SparQl 😉

    #nanopub #Snakemake

  42. Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: w3id.org/np/RAzeQbv1gXqKIuLic4

    Not yet sophisticated, but I am starting to like #SparQl 😉

    #nanopub #Snakemake

  43. Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: w3id.org/np/RAzeQbv1gXqKIuLic4

    Not yet sophisticated, but I am starting to like #SparQl 😉

    #nanopub #Snakemake

  44. Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: w3id.org/np/RAzeQbv1gXqKIuLic4

    Not yet sophisticated, but I am starting to like #SparQl 😉

    #nanopub #Snakemake

  45. Just published a nanopublication to list all other nanopubs mentioning the Snakemake Workflow Management System: w3id.org/np/RAzeQbv1gXqKIuLic4

    Not yet sophisticated, but I am starting to like #SparQl 😉

    #nanopub #Snakemake