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From: Christoph S. <chr...@un...> - 2024-01-24 10:26:17
|
Dear all, we are organising a week-long retreat on deep learning in molecular informatics as part of a workshop series called International Workshop on Open Molecular Informatics (IWOMI) from 13.-17. May 2024. The meeting place is located in the mountains next to Bolzano in Italy and a wonderful place to retreat and enjoy hands-on tutorials, hackathons and scientific and non-scientific conversations. This 2024 meeting will feature scientific talks, a hands-on session to learn how to train deep learning models using the Google Cloud and how to re-train GPT models for your specific scientific application. We will also have time for hackathons and a hike in the mountains. If you are interested, please register at https://www.iwomi.net/ and let me know if you would like to contribute a talk, tutorial, or a hackathon session. The registration deadline is the end of February. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Vice President for Digitalisation of the Friedrich-Schiller-University Jena Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Team Assistant: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@un...> - 2023-04-12 12:30:43
|
Dear all, AstraZeneca in Cambridge, UK, is looking for a hit discovery data scientist to help maximise the value of their internal datasets and build predictive models to better inform present/future campaigns and compounds collections for screening. This may be of interest for small molecule data science and ML/AI colleagues reaching the end of contract or looking for new career possibilities. Applications are open until the 19th April. AZ careers website: https://careers.astrazeneca.com/job/cambridge/senior-data-scientist-hit-discovery/7684/46662940032 Linkedin: https://www.linkedin.com/posts/clairemayo_datascience-hitdiscovery-smallmolecules-activity-7046799144765534209-ITA0 Kind regards, Chris — Prof. Dr. Christoph Steinbeck Vice President for Digitalisation of the Friedrich-Schiller-University Jena Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Team Assistant: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@un...> - 2023-01-08 10:00:21
|
Hi Suliman, > Is there some travel scholarship I can apply for to attend this workshop from the US? not from any organisation affiliated with this meeting. But there are travel grants from learned societies such as the ACS, AFAIK. There is also the travel grants from the CSA trust that you could give a try. (https://csa-trust.org/awards-and-grants/grants/) Kind regards, Chris — Prof. Dr. Christoph Steinbeck Vice President for Digitalisation of the Friedrich-Schiller-University Jena Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Team Assistant: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 7. Jan 2023, at 14:27, Suliman Sharif <sha...@gm...> wrote: > > Hey All, > > Is there some travel scholarship I can apply for to attend this workshop from the US? > > -Sul > > On Sat, Jan 7, 2023 at 7:36 AM Christoph Steinbeck <chr...@un...> wrote: > Dear all, > > we are organising a meeting on cross-toolkit structure registration and normalization a part of a new workshop series called IWOMI. > > You can find more information about this year's International Workshop on Open Molecular Information (IWOMI) at https://www.iwomi.net. > If you are interested to join, please register on the workshop webpage. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Vice President for Digitalisation of the Friedrich-Schiller-University Jena > > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Team Assistant: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > _______________________________________________ > Blueobelisk-discuss mailing list > Blu...@li... > https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss > > > -- > Suliman Sharif > Ph.D. Candidate Pharmaceutical Sciences | University of Maryland, School of Pharmacy > M.Sc Medicinal Chemistry | University of California, Riverside School of Medicine > B.Sc. Biochemistry | University of Texas at Austin > sha...@gm... |
From: Christoph S. <chr...@un...> - 2023-01-07 12:36:09
|
Dear all, we are organising a meeting on cross-toolkit structure registration and normalization a part of a new workshop series called IWOMI. You can find more information about this year's International Workshop on Open Molecular Information (IWOMI) at https://www.iwomi.net. If you are interested to join, please register on the workshop webpage. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Vice President for Digitalisation of the Friedrich-Schiller-University Jena Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Team Assistant: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@un...> - 2022-02-04 08:58:29
|
Hi Tim, sorry for confusing you. I took your email as an occasion to update the google group that we created for the very first attempt to get this meeting organised in 2020 when the whole crap started. Let’s move the discussion there. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 3. Feb 2022, at 20:53, Tim Dudgeon <tdu...@gm...> wrote: > > Where is the right place for discussions on this event to happen? I'm pretty confused (but registered, and booked). > > On Wed, Jan 19, 2022 at 10:31 AM Christoph Steinbeck <chr...@un...> wrote: > Dear all, > > as announced last November on this list, the CDK 20th anniversary workshop will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022. > > We are reaching the end of the registration period with the hotel, which is tomorrow. They might be able to hold the rooms for a tiny little longer, but there is no guarantee. At the moment, there are 20 rooms left. > The closer we get to the event, the more we compete with the regular guests for rooms. > Please consider booking ASAP if you are interested to join. It is really nice there :) > > For more information including how to register please visit > > https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647 > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user |
From: Egon W. <ego...@gm...> - 2022-01-19 11:38:49
|
Thanks for the reminder! Egon On Wed, 19 Jan 2022 at 11:30, Christoph Steinbeck < chr...@un...> wrote: > Dear all, > > as announced last November on this list, the CDK 20th anniversary workshop > will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022. > > We are reaching the end of the registration period with the hotel, which > is tomorrow. They might be able to hold the rooms for a tiny little longer, > but there is no guarantee. At the moment, there are 20 rooms left. > The closer we get to the event, the more we compete with the regular > guests for rooms. > Please consider booking ASAP if you are interested to join. It is really > nice there :) > > For more information including how to register please visit > > > https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647 > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- ---- BiGCaT received a NWO Open Science grant to support our research into interoperability of biological data and knowledge: https://www.nature.com/articles/d41586-021-03418-1 and https://www.nwo.nl/en/researchprogrammes/open-science/open-science-fund/open-science-fund-2021-awarded-grants ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> / @egonw <https://scholar.social/@egonw> Homepage: http://egonw.github.io/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen |
From: Christoph S. <chr...@un...> - 2022-01-19 10:30:45
|
Dear all, as announced last November on this list, the CDK 20th anniversary workshop will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022. We are reaching the end of the registration period with the hotel, which is tomorrow. They might be able to hold the rooms for a tiny little longer, but there is no guarantee. At the moment, there are 20 rooms left. The closer we get to the event, the more we compete with the regular guests for rooms. Please consider booking ASAP if you are interested to join. It is really nice there :) For more information including how to register please visit https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647 Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@un...> - 2021-11-23 15:05:33
|
Dear all, the CDK 20th anniversary workshop will be held on Schloss Korb near Bolzano, Italy, from 4. - 8. April 2022. For more information including how to register please visit https://www.eventbrite.co.uk/e/cdk-20th-anniversary-symposium-tickets-215520175647 Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Egon W. <ego...@gm...> - 2021-08-24 07:48:31
|
Thanks, Chris! Egon On Tue, Aug 24, 2021 at 8:44 AM Christoph Steinbeck < chr...@un...> wrote: > Hi Egon, > > I wrote to Schloss Korb yesterday, confirming the April date. They did not > yet write back but I assume it will be ok. > > Kind regards, > > Chris > > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Institute for Inorganic and Analytical Chemistry > Friedrich-Schiller-University > Lessingstr. 8, D-07743 Jena, Germany > Phone Secretariat: +49-3641-948171 > Email: chr...@un... > http://orcid.org/0000-0001-6966-0814 > > Am 24.08.2021 um 08:30 schrieb Egon Willighagen < > ego...@gm...>: > > > > Chris, > > I like to go ahead with inviting the Dagstuhl invitation, but only if the > CDK meeting is confirmed in April. > > On Wed, Aug 11, 2021 at 5:15 PM Egon Willighagen < > ego...@gm...> wrote: > >> Ah, indeed it does. >> > > Egon > > > -- > This year I am stepping down as co-Editor-in-Chief of the Journal of > Cheminformatics, because of a conflict of interest with Springer Nature. > See https://twitter.com/egonwillighagen/status/1403299501947899907 > > ----- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> > / @egonw <https://scholar.social/@egonw> > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> > ImpactStory: https://impactstory.org/u/egonwillighagen > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> / @egonw <https://scholar.social/@egonw> Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen |
From: Christoph S. <chr...@un...> - 2021-08-24 06:44:43
|
Hi Egon, I wrote to Schloss Korb yesterday, confirming the April date. They did not yet write back but I assume it will be ok. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Lessingstr. 8, D-07743 Jena, Germany Phone Secretariat: +49-3641-948171 Email: chr...@un... http://orcid.org/0000-0001-6966-0814 > Am 24.08.2021 um 08:30 schrieb Egon Willighagen <ego...@gm...>: > > > > Chris, > > I like to go ahead with inviting the Dagstuhl invitation, but only if the CDK meeting is confirmed in April. > >> On Wed, Aug 11, 2021 at 5:15 PM Egon Willighagen <ego...@gm...> wrote: >> Ah, indeed it does. > > Egon > > > -- > This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 > > ----- > E.L. Willighagen > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Twitter/Mastodon: @egonwillighagen / @egonw > Homepage: http://egonw.github.com/ > Blog: http://chem-bla-ics.blogspot.com/ > PubList: https://www.zotero.org/egonw > ORCID: 0000-0001-7542-0286 > ImpactStory: https://impactstory.org/u/egonwillighagen > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Egon W. <ego...@gm...> - 2021-08-24 06:30:37
|
Chris, I like to go ahead with inviting the Dagstuhl invitation, but only if the CDK meeting is confirmed in April. On Wed, Aug 11, 2021 at 5:15 PM Egon Willighagen <ego...@gm...> wrote: > Ah, indeed it does. > Egon -- This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> / @egonw <https://scholar.social/@egonw> Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen |
From: Egon W. <ego...@gm...> - 2021-08-11 15:15:45
|
Ah, indeed it does. Egon On Wed, Aug 11, 2021 at 4:27 PM Maria Sorokina <mar...@gm...> wrote: > Dear Chris, > > Just for your information, the Dagstuhl seminar will be apparently from > 1st to 6th of May 2022, next year (i.e. overlapping with the May date for > the CDK). > > Kind regards, > Maria > > Dr. Maria Sorokina > Steinbeck Research Group > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > https://naturalproducts.net/ > http://cheminf.uni-jena.de > Le 11 août 2021 à 14:47 +0200, Christoph Steinbeck < > chr...@un...>, a écrit : > > Dear all, > > due to a misunderstanding with the hotel, I had to extend the poll with > another option. > The date in May would actually start on Sunday, 1. May, and end on the > Thursday. Since I want to avoid us waisting a precious day of the weekend, > the hotel opened another slot for us in early April: > > Kindly re-visit the poll at https://doodle.com/poll/pdmaypfixthw7tpy and > make new choices. Apologies for the trouble. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > On 2. Aug 2021, at 11:40, Christoph Steinbeck < > chr...@un...> wrote: > > Dear all, > > we had an excellent, small and rebranded meeting on Schloss Korb from July > 12-16. This should have been the CDK 20th anniversary workshop but as you > all know, many of you could not make it (again, we already tried in 2020) > due to COVID restrictions. > Since this meeting with 14 participants worked very well, I dare to start > planning for the full CDK 20y event again next year :) > > After consultation with the hotel, the week from 2 May to 6 May 2022 would > very well. > Can you please indicate in the following poll if you are interested to > join? > This is a yes/no/if-need-be poll, so please feel free to also indicate if > you cannot join or would maybe join. This helps us to understand the demand > better. > > https://doodle.com/poll/pdmaypfixthw7tpy > > The old meeting page about the previous attempts for the meeting are here: > > https://www.eventbrite.co.uk/e/open-cheminformatics-of-natural-products-and-metabolites-tickets-62840183681 > for your information. > > If enough people indicate interest, I will create a new meeting page. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > -- This year I am stepping down as co-Editor-in-Chief of the Journal of Cheminformatics, because of a conflict of interest with Springer Nature. See https://twitter.com/egonwillighagen/status/1403299501947899907 ----- E.L. Willighagen Department of Bioinformatics - BiGCaT Maastricht University (http://www.bigcat.unimaas.nl/) Twitter/Mastodon: @egonwillighagen <https://twitter.com/egonwillighagen> / @egonw <https://scholar.social/@egonw> Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: https://www.zotero.org/egonw ORCID: 0000-0001-7542-0286 <http://orcid.org/0000-0001-7542-0286> ImpactStory: https://impactstory.org/u/egonwillighagen |
From: Maria S. <mar...@gm...> - 2021-08-11 14:27:12
|
Dear Chris, Just for your information, the Dagstuhl seminar will be apparently from 1st to 6th of May 2022, next year (i.e. overlapping with the May date for the CDK). Kind regards, Maria Dr. Maria Sorokina Steinbeck Research Group Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany https://naturalproducts.net/ http://cheminf.uni-jena.de Le 11 août 2021 à 14:47 +0200, Christoph Steinbeck <chr...@un...>, a écrit : > Dear all, > > due to a misunderstanding with the hotel, I had to extend the poll with another option. > The date in May would actually start on Sunday, 1. May, and end on the Thursday. Since I want to avoid us waisting a precious day of the weekend, the hotel opened another slot for us in early April: > > Kindly re-visit the poll at https://doodle.com/poll/pdmaypfixthw7tpy and make new choices. Apologies for the trouble. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > On 2. Aug 2021, at 11:40, Christoph Steinbeck <chr...@un...> wrote: > > > > Dear all, > > > > we had an excellent, small and rebranded meeting on Schloss Korb from July 12-16. This should have been the CDK 20th anniversary workshop but as you all know, many of you could not make it (again, we already tried in 2020) due to COVID restrictions. > > Since this meeting with 14 participants worked very well, I dare to start planning for the full CDK 20y event again next year :) > > > > After consultation with the hotel, the week from 2 May to 6 May 2022 would very well. > > Can you please indicate in the following poll if you are interested to join? > > This is a yes/no/if-need-be poll, so please feel free to also indicate if you cannot join or would maybe join. This helps us to understand the demand better. > > > > https://doodle.com/poll/pdmaypfixthw7tpy > > > > The old meeting page about the previous attempts for the meeting are here: > > https://www.eventbrite.co.uk/e/open-cheminformatics-of-natural-products-and-metabolites-tickets-62840183681 > > for your information. > > > > If enough people indicate interest, I will create a new meeting page. > > > > Kind regards, > > > > Chris > > > > — > > Prof. Dr. Christoph Steinbeck > > Analytical Chemistry - Cheminformatics and Chemometrics > > Friedrich-Schiller-University Jena, Germany > > Phone Secretariat: +49-3641-948171 > > http://cheminf.uni-jena.de > > http://orcid.org/0000-0001-6966-0814 > > > > What is man but that lofty spirit - that sense of enterprise. > > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Christoph S. <chr...@un...> - 2021-08-11 12:47:03
|
Dear all, due to a misunderstanding with the hotel, I had to extend the poll with another option. The date in May would actually start on Sunday, 1. May, and end on the Thursday. Since I want to avoid us waisting a precious day of the weekend, the hotel opened another slot for us in early April: Kindly re-visit the poll at https://doodle.com/poll/pdmaypfixthw7tpy and make new choices. Apologies for the trouble. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 2. Aug 2021, at 11:40, Christoph Steinbeck <chr...@un...> wrote: > > Dear all, > > we had an excellent, small and rebranded meeting on Schloss Korb from July 12-16. This should have been the CDK 20th anniversary workshop but as you all know, many of you could not make it (again, we already tried in 2020) due to COVID restrictions. > Since this meeting with 14 participants worked very well, I dare to start planning for the full CDK 20y event again next year :) > > After consultation with the hotel, the week from 2 May to 6 May 2022 would very well. > Can you please indicate in the following poll if you are interested to join? > This is a yes/no/if-need-be poll, so please feel free to also indicate if you cannot join or would maybe join. This helps us to understand the demand better. > > https://doodle.com/poll/pdmaypfixthw7tpy > > The old meeting page about the previous attempts for the meeting are here: > https://www.eventbrite.co.uk/e/open-cheminformatics-of-natural-products-and-metabolites-tickets-62840183681 > for your information. > > If enough people indicate interest, I will create a new meeting page. > > Kind regards, > > Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > |
From: Christoph S. <chr...@un...> - 2021-08-02 09:41:17
|
Dear all, we had an excellent, small and rebranded meeting on Schloss Korb from July 12-16. This should have been the CDK 20th anniversary workshop but as you all know, many of you could not make it (again, we already tried in 2020) due to COVID restrictions. Since this meeting with 14 participants worked very well, I dare to start planning for the full CDK 20y event again next year :) After consultation with the hotel, the week from 2 May to 6 May 2022 would very well. Can you please indicate in the following poll if you are interested to join? This is a yes/no/if-need-be poll, so please feel free to also indicate if you cannot join or would maybe join. This helps us to understand the demand better. https://doodle.com/poll/pdmaypfixthw7tpy The old meeting page about the previous attempts for the meeting are here: https://www.eventbrite.co.uk/e/open-cheminformatics-of-natural-products-and-metabolites-tickets-62840183681 for your information. If enough people indicate interest, I will create a new meeting page. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Jonas S. <jon...@un...> - 2021-07-22 19:35:22
|
Dear CDK-developers, I am a PhD student in Christoph Steinbeck's group and I have been involved in two projects that might be interesting for integration into the CDK. The first one is the ErtlFunctionalGroupsFinder, an open, CDK-based implementation of Peter Ertl's algorithm for functional group detection<https://doi.org/10.1186/s13321-017-0225-z>. Our implementation is described in this paper<https://doi.org/10.1186/s13321-019-0361-8> and the source code can be found here<https://github.com/zielesny/ErtlFunctionalGroupsFinder>. Getting it into CDK would require integrating one principal class implementing the functionality, a corresponding test class (these two can be found here<https://github.com/zielesny/ErtlFunctionalGroupsFinder/tree/master/Basic>), and (if you agree) a utility class with some convenient routines for pre-and postprocessing in a workflow using ErtlFunctionalGroupsFinder. The utility class along with its test class can be found here<https://github.com/zielesny/ErtlFunctionalGroupsFinder/tree/master/Utility>. The second project is named Sugar Removal Utility, an open, CDK-based implementation of an algorithm for in silico deglycosylation. We have described the algorithm and its implementation in this paper<https://doi.org/10.1186/s13321-020-00467-y><https://jcheminf.biomedcentral.com/articles/10.1186/s13321-020-00467-y><https://doi.org/10.1186/s13321-020-00467-y> and used it for the project described here<https://doi.org/10.3390/biom11040486> that illustrates its possibilities and configurations in more detail. The source code can be found here<https://github.com/JonasSchaub/SugarRemoval>. As far as we know, there is no deglycosylation functionality in CDK, only a CDK-based KNIME node for this purpose<https://github.com/cdk/nodes4knime/tree/master/org.openscience.cdk.knime/src/org/openscience/cdk/knime/nodes/sugarremover>. The Sugar Removal Utility consists of one principal class<https://github.com/JonasSchaub/SugarRemoval/blob/master/src/main/java/de/unijena/cheminf/deglycosylation/SugarRemovalUtility.java> implementing the functionality and a corresponding test class<https://github.com/JonasSchaub/SugarRemoval/blob/master/src/test/java/de/unijena/cheminf/deglycosylation/SugarRemovalUtilityTest.java>. In the latter, a few test methods would have to be removed that illustrate the deglycosylation results on a small test data set and test the surrounding command-line application. Do you think these two projects should be integrated into the CDK? Do you want me to create a pull request on GitHub (or rather two separate ones)? Would you request any changes to the code? I would be happy to give more details on specific aspects of the two projects or discuss any required code changes. Kind regards, Jonas Schaub ___________ Jonas Schaub jon...@un...<mailto:jon...@un...> http://orcid.org/0000-0003-1554-6666 Doctoral candidate of Steinbeck Research Group Friedrich-Schiller-University Jena, Germany http://cheminf.uni-jena.de Institute for Analytical Chemistry Lessingstr. 8 07743 Jena |
From: Christoph S. <chr...@un...> - 2020-10-26 10:17:51
|
Dear all, Greg Landrum just announced on the RDKit discussion list that: > The individual videos from the 2020 RDKit UGM are now up on YouTube: > https://www.youtube.com/playlist?list=PLugOo5eIVY3HW8kJYnoBNyJvg8P6qtl44 No doubt that a lot of them are also interesting for our community. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@gm...> - 2020-08-27 11:14:25
|
Dear all, I take the freedom to alert you of a blog post of by RDKit icon Greg Landrum on similarity searching with highly folded fingerprints. Also with nice link to an in-memory GPU-based similarity search. http://rdkit.blogspot.com/2020/08/doing-similarity-searches-with-highly.html Very practical and stuff to think about. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Institute for Inorganic and Analytical Chemistry Friedrich-Schiller-University Lessingstr. 8, D-07743 Jena, Germany Phone Secretariat: +49-3641-948171 Email: chr...@un... http://orcid.org/0000-0001-6966-0814 |
From: Christoph S. <chr...@un...> - 2019-11-06 10:55:34
|
Dear all, for all of you who have registered interest to participate in the CDK 20y anniversary symposium on Schloss Korb but did not register yet for the event. At the moment, we have around 20 registrations, so it is certainly going to be a fun event with good participation. The hotel has only reserved rooms for us until early November (now), so if you still want to join, you should act soon. This is a moderately remote location, so you don’t want to be in another hotel :) Again, the registration page is at http://cdk20y.org. IMPORTANT: It is a 2-step registration. Read the information at http://cdk20y.org carefully. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 3. Aug 2019, at 17:07, Christoph Steinbeck <chr...@un...> wrote: > > Dear all, > > following our poll in May this year, a good number people indicated interest in participating in celebrating the 20th anniversary of the Chemistry Development Kit (CDK) next year in a symposium. > The symposium will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. > > I am now delighted to inform you that the negotiations with Hotel Schloss Korb are finalised and that the registration is open at http://cdk20y.org. > Please read the registration page carefully - it is a 2-step process involving an immediate registration at the Eventbrite site and then you must book your own room with the hotel. The hotel rooms are only held for us until end of October 2019! > Due to the particularity of the remote location, a stay at another hotel is not foreseen. > > Kind regards, Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > >> On 23. May 2019, at 12:10, Christoph Steinbeck <chr...@un...> wrote: >> >> Dear all, >> >> we are planning to have a symposium to celebrate the 20th anniversary of the Chemistry Development Kit (CDK). >> It will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. >> We would be delighted to celebrate this occasion also with friends and colleagues from other open source projects in cheminformatics. >> >> To help us plan the size of the events and to ask the hotel to block an appropriate amount of rooms, we would like to poll your interest to participate. >> Indicating your interest does not constitute a booking or a later obligation to participate. We will open a registration page later this years. >> More information is also included in the following poll. >> You can always revisit this poll in the future and change your choice. >> >> https://doodle.com/poll/cy66agk2kzqby6eq >> >> Please do also forward the link to interested other parties. >> >> Kind regards, Chris >> >> — >> Prof. Dr. Christoph Steinbeck >> Analytical Chemistry - Cheminformatics and Chemometrics >> Friedrich-Schiller-University Jena, Germany >> Phone Secretariat: +49-3641-948171 >> http://cheminf.uni-jena.de >> http://orcid.org/0000-0001-6966-0814 >> >> What is man but that lofty spirit - that sense of enterprise. >> ... Kirk, "I, Mudd," stardate 4513.3.. >> >> >> >> _______________________________________________ >> Cdk-devel mailing list >> Cdk...@li... >> https://lists.sourceforge.net/lists/listinfo/cdk-devel > |
From: Syed A. R. <s9...@gm...> - 2019-09-08 08:47:21
|
Great idea Chris! One of my favourite paper on Chemical reaction classification based on the Bond Electron matrix is “An Algebraic Model of Constitutional Chemistry as a Basis for Chemical Computer Programs” 1973 by Prof. Dr. James Dugundji and Prof. Dr. Ivar Ugi -Asad Sent from my iPhone Apologies for any typos > On 3 Sep 2019, at 16:48, Craig James <cj...@em...> wrote: > > > >> On Mon, Sep 2, 2019 at 6:01 AM Christoph Steinbeck <chr...@un...> wrote: >> >> for teaching and documentation purposes, I would like to compile, with your help, a list of seminal papers in cheminformatics. >> It could be hosted on BlueOblisk.org and be a guidance for teaching and learning. > > A good resource for this could be John Bradshaw and David Livingston's chapter, "A History of the Development of Data Mining in Pharmaceutical Research". John was an avid science historian and gave a really fun talk at Daylight one year. I haven't read the Wiley book, but I imagine it has a lot of good references and is a thorough history. > > Craig > > -- > --------------------------------- > Craig A. James > Chief Technology Officer > eMolecules, Inc. > 3430 Carmel Mountain Road, Suite 250 > San Diego, CA 92121 > --------------------------------- > _______________________________________________ > Cdk-user mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-user |
From: Craig J. <cj...@em...> - 2019-09-03 16:13:17
|
On Mon, Sep 2, 2019 at 6:01 AM Christoph Steinbeck < chr...@un...> wrote: > > for teaching and documentation purposes, I would like to compile, with > your help, a list of seminal papers in cheminformatics. > It could be hosted on BlueOblisk.org and be a guidance for teaching and > learning. > A good resource for this could be John Bradshaw and David Livingston's chapter, "A History of the Development of Data Mining in Pharmaceutical Research <https://onlinelibrary.wiley.com/doi/pdf/10.1002/9780470567623.ch1>". John was an avid science historian and gave a really fun talk at Daylight one year. <https://www.daylight.com/meetings/mug01/Bradshaw/History/1024x768/Strings_and_Things/sld001.htm> I haven't read the Wiley book, but I imagine it has a lot of good references and is a thorough history. Craig -- --------------------------------- Craig A. James Chief Technology Officer eMolecules, Inc. 3430 Carmel Mountain Road, Suite 250 San Diego, CA 92121 --------------------------------- |
From: Christoph S. <chr...@un...> - 2019-09-02 13:01:22
|
Dear all, for teaching and documentation purposes, I would like to compile, with your help, a list of seminal papers in cheminformatics. It could be hosted on BlueOblisk.org and be a guidance for teaching and learning. It would be great if you could contribute. Please add your favorite paper as a citation to the following spreadsheet, ideally also adding the DOI for de-duplication: https://docs.google.com/spreadsheets/d/1erXgdfpqOegSWbdevLsYwKU5feQLa0OGA4Rvf7MhV_U/edit?usp=sharing After a collection phase of 14 days, I would then have a voting phase and eventually publish the ranked list on the Blue Obelisk page. Could be added to the Wikipedia page of Cheminformatics too. This poll could be later be compared with a bibliometric analysis. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Christoph S. <chr...@un...> - 2019-08-03 15:07:31
|
Dear all, following our poll in May this year, a good number people indicated interest in participating in celebrating the 20th anniversary of the Chemistry Development Kit (CDK) next year in a symposium. The symposium will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. I am now delighted to inform you that the negotiations with Hotel Schloss Korb are finalised and that the registration is open at http://cdk20y.org. Please read the registration page carefully - it is a 2-step process involving an immediate registration at the Eventbrite site and then you must book your own room with the hotel. The hotel rooms are only held for us until end of October 2019! Due to the particularity of the remote location, a stay at another hotel is not foreseen. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. > On 23. May 2019, at 12:10, Christoph Steinbeck <chr...@un...> wrote: > > Dear all, > > we are planning to have a symposium to celebrate the 20th anniversary of the Chemistry Development Kit (CDK). > It will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. > We would be delighted to celebrate this occasion also with friends and colleagues from other open source projects in cheminformatics. > > To help us plan the size of the events and to ask the hotel to block an appropriate amount of rooms, we would like to poll your interest to participate. > Indicating your interest does not constitute a booking or a later obligation to participate. We will open a registration page later this years. > More information is also included in the following poll. > You can always revisit this poll in the future and change your choice. > > https://doodle.com/poll/cy66agk2kzqby6eq > > Please do also forward the link to interested other parties. > > Kind regards, Chris > > — > Prof. Dr. Christoph Steinbeck > Analytical Chemistry - Cheminformatics and Chemometrics > Friedrich-Schiller-University Jena, Germany > Phone Secretariat: +49-3641-948171 > http://cheminf.uni-jena.de > http://orcid.org/0000-0001-6966-0814 > > What is man but that lofty spirit - that sense of enterprise. > ... Kirk, "I, Mudd," stardate 4513.3.. > > > > _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel |
From: Christoph S. <chr...@un...> - 2019-05-23 10:11:08
|
Dear all, we are planning to have a symposium to celebrate the 20th anniversary of the Chemistry Development Kit (CDK). It will be from 11. - 15. May 2020 at Schloss Korb in the Tyrolean mountains close to Bolzano. We would be delighted to celebrate this occasion also with friends and colleagues from other open source projects in cheminformatics. To help us plan the size of the events and to ask the hotel to block an appropriate amount of rooms, we would like to poll your interest to participate. Indicating your interest does not constitute a booking or a later obligation to participate. We will open a registration page later this years. More information is also included in the following poll. You can always revisit this poll in the future and change your choice. https://doodle.com/poll/cy66agk2kzqby6eq Please do also forward the link to interested other parties. Kind regards, Chris — Prof. Dr. Christoph Steinbeck Analytical Chemistry - Cheminformatics and Chemometrics Friedrich-Schiller-University Jena, Germany Phone Secretariat: +49-3641-948171 http://cheminf.uni-jena.de http://orcid.org/0000-0001-6966-0814 What is man but that lofty spirit - that sense of enterprise. ... Kirk, "I, Mudd," stardate 4513.3.. |
From: Kohulan R. <koh...@gm...> - 2019-04-29 15:41:11
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Dear John, Thank you for the explanation. Post layout rescaling is more than enough for my problem and it works well for me. Kind regards, Kohulan.R “It is our choices that show what we truly are, far more than our abilities.” - Albus Dumbledore On Mon, Apr 29, 2019, 5:30 PM John Mayfield <joh...@gm...> wrote: > Urgh, typing busy day. Basically the default should do what you want, if > you set changes parameters it will sometimes make things bigger or smaller > because it has to. > > On Mon, 29 Apr 2019 at 16:27, John Mayfield <joh...@gm...> > wrote: > >> Again, this should be the default. Do you have an example of your code I >> think you're setting something you shouldn't or misreading one of the >> parameters? >> >> For vector graphics it will render bond lengths as ACS 1996 style >> guidelines, the values is in Pt. >> For Raster graphics it will rendering everything as 40px bond length. >> >> If the diagraph is too big for the specified size it will shrink it, >> because it can't do anything else. If you don't specify a size it will just >> make it as big as it wants with fixed bond lengths. It will only big a >> depiction bigger if "zoom to fit" is set to true, default is false. >> >> On Mon, 29 Apr 2019 at 10:58, Kohulan Rajan <koh...@gm...> wrote: >> >>> Dear John, >>> >>> Thanks for the reply. I have already done the post layout rescaling. >>> >>> Without setting a fixed size to the molecules the bigger molecules try >>> to shrink to fit the canvas size, which we don't want. we need to depict >>> all the molecules in our dataset with the same bond length in fixed canvas >>> size, so the molecules will have the same size irrespective of the canvas. >>> >>> Kind regards, >>> Kohulan >>> >>> “It is our choices that show what we truly are, far more than our >>> abilities.” - Albus Dumbledore >>> >>> >>> >>> On Sun, Apr 28, 2019 at 10:24 PM John Mayfield < >>> joh...@gm...> wrote: >>> >>>> >>>> http://cdk.github.io/cdk/2.2/docs/api/org/openscience/cdk/layout/StructureDiagramGenerator.html#setBondLength-double- >>>> >>>> But as it says you're better off doing a post layout re-scale, the bond >>>> length is only a hint as some bonds will be stretch/shrunk to fit. Do you >>>> have an particular example of why you want to change it? >>>> >>>> On Sun, 28 Apr 2019 at 09:48, Kohulan Rajan <koh...@gm...> >>>> wrote: >>>> >>>>> Dear CDK Developers, >>>>> >>>>> Is there a way to set the bond length of the molecules in Depiction >>>>> generator in order to depict all molecules with same bond lengths? >>>>> >>>>> Kind regards, >>>>> Kohulan >>>>> >>>>> _______________________________________________ >>>>> Cdk-devel mailing list >>>>> Cdk...@li... >>>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>>> >>>> _______________________________________________ >>>> Cdk-devel mailing list >>>> Cdk...@li... >>>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>>> >>> _______________________________________________ >>> Cdk-devel mailing list >>> Cdk...@li... >>> https://lists.sourceforge.net/lists/listinfo/cdk-devel >>> >> _______________________________________________ > Cdk-devel mailing list > Cdk...@li... > https://lists.sourceforge.net/lists/listinfo/cdk-devel > |