Next Wednesday! Genomic data science with the Galaxy workbench @ SACNAS
Hello All, We have less than a week to go before the Genomic data science with the Galaxy workbench <https://galaxyproject.org/events/2019-sacnas> pre-conference workshop at SACNAS. The workshop will be held Wednesday, October 30, 9am- 6pm in room 318AB at the Hawai’l Convention Center. Breaks (but not lunch - sorry, we could not afford it) will be provided. Here’s what you need to know for next Wednesday. Laptop The workshop will be hands-on! Please bring a fully charged,* wifi-enabled laptop with Firefox or Chrome already installed on it. Cancellation? This workshop is full, but people still want to attend. Please let us know as soon as possible if you can no longer make it. We Switched Examples We have switched our example analysis to differential gene expression (DGE). DGE is about figuring out what genes are turned on when. We had originally proposed using a genome wide association study (GWAS) as the example problem. GWAS was new to us, and after having explored that space we have decided that GWAS is not yet ready for a workshop. So 1. Don’t worry if none of the details above mean anything to you. We need a sample problem to work on and we have switched to a better one. 2. However, if you are keen to learn more about GWAS, we would be happy to discuss it with you over breaks and during the rest of SACNAS. Communication! We have set up two channels for communication. 1. This mailing list. We’ll use it to send out information that needs to go to everyone. 2. A workshop chat channel on Gitter.im: https://gitter.im/galaxyproject/SACNAS-2019. Please use this for chat. We’ll use this for communication (for example, links) during the workshop, and for any discussion that doesn’t need to go to everyone, right now. You are already a member of the mailing list. And you can already see everything posted on chat. However, if you want to post something to chat, you will need to login to Gitter with either your GitHub**, GitLab, or Twitter ID***. Please let us know if you have any questions, and we will see you on Gitter, and in Honolulu next week, Mo H and Dave C --- * We aren’t sure of the power situation yet. ** Why you should be on GitHub (or GitLab)! If you don’t already have a GitHub <https://github.com/> (or GitLab) account then we strongly recommend getting one. Data science happens with Git <https://git-scm.com/>, and GitHub is the most popular platform for using Git. You won’t need to understand Git to understand this workshop. *** Why you should be on Twitter We can’t speak to disciplines outside of life sciences, but for life sciences these two quotes reflect the importance of Twitter in these fields: - Twitter is one of the most important bioinformatics tools you can use. <https://www.dnalc.org/about/staff/williams.html> Jason Williams <https://www.dnalc.org/about/staff/williams.html>, CSHL & CyVerse - Twitter is the world's largest lab meeting. Someone at PAG <https://www.intlpag.org/>, several years ago -- https://galaxyproject.org/
Hello all, We have just 3 days to go! Some updates: *Laptop* In addition to Chrome or Firefox, *please also install RStudio Desktiop* <https://rstudio.com/products/rstudio/download/>. Thanks to Ben Clarke for pointing this omission out. *Code of Conduct* SACNAS has a code of conduct <https://www.2019sacnas.org/code-of-conduct/>. Please review and abide by it. *We have a cancellation to fill* We have had two last minute cancellations. We have managed to fill one of them (Comet, welcome aboard, and please let me know if you get this email). However, we need help filling that last slot. *If you know anyone who will be in Honolulu on Wednesday and would benefit from this workshop*, then please let Mo and I know as soon as possible. See you Wednesday, Dave C On Thu, Oct 24, 2019 at 1:06 PM Dave Clements <clementsgalaxy@gmail.com> wrote:
Hello All,
We have less than a week to go before the Genomic data science with the Galaxy workbench <https://galaxyproject.org/events/2019-sacnas> pre-conference workshop at SACNAS. The workshop will be held Wednesday, October 30, 9am- 6pm in room 318AB at the Hawai’l Convention Center. Breaks (but not lunch - sorry, we could not afford it) will be provided.
Here’s what you need to know for next Wednesday.
Laptop
The workshop will be hands-on! Please bring a fully charged,* wifi-enabled laptop with Firefox or Chrome already installed on it.
Cancellation?
This workshop is full, but people still want to attend. Please let us know as soon as possible if you can no longer make it.
We Switched Examples
We have switched our example analysis to differential gene expression (DGE). DGE is about figuring out what genes are turned on when. We had originally proposed using a genome wide association study (GWAS) as the example problem. GWAS was new to us, and after having explored that space we have decided that GWAS is not yet ready for a workshop.
So
1.
Don’t worry if none of the details above mean anything to you. We need a sample problem to work on and we have switched to a better one. 2.
However, if you are keen to learn more about GWAS, we would be happy to discuss it with you over breaks and during the rest of SACNAS.
Communication!
We have set up two channels for communication.
1. This mailing list. We’ll use it to send out information that needs to go to everyone.
2. A workshop chat channel on Gitter.im: https://gitter.im/galaxyproject/SACNAS-2019. Please use this for chat. We’ll use this for communication (for example, links) during the workshop, and for any discussion that doesn’t need to go to everyone, right now.
You are already a member of the mailing list. And you can already see everything posted on chat. However, if you want to post something to chat, you will need to login to Gitter with either your GitHub**, GitLab, or Twitter ID***.
Please let us know if you have any questions, and we will see you on Gitter, and in Honolulu next week,
Mo H and Dave C
---
* We aren’t sure of the power situation yet.
** Why you should be on GitHub (or GitLab)!
If you don’t already have a GitHub <https://github.com/> (or GitLab) account then we strongly recommend getting one. Data science happens with Git <https://git-scm.com/>, and GitHub is the most popular platform for using Git. You won’t need to understand Git to understand this workshop.
*** Why you should be on Twitter
We can’t speak to disciplines outside of life sciences, but for life sciences these two quotes reflect the importance of Twitter in these fields:
-
Twitter is one of the most important bioinformatics tools you can use. <https://www.dnalc.org/about/staff/williams.html>
Jason Williams <https://www.dnalc.org/about/staff/williams.html>, CSHL & CyVerse
-
Twitter is the world's largest lab meeting.
Someone at PAG <https://www.intlpag.org/>, several years ago
Hello Dave, Unfortunately I was ill and unable to fly this evening as planned, so will not be able to attend the workshop tomorrow. I am SO disappointed to miss it! Thank you for your help, hopefully you’ll have/I can attend a WS at the SACNAS conference next year in Long Beach. All the best, Marla Robinson FT Biology Faculty Seattle Central College Office: SAM314 | Ph. 206.934.6989 ________________________________ From: Dave Clements <clementsgalaxy@gmail.com> Sent: Sunday, October 27, 2019 7:05:14 PM To: Galaxy SACNAS 2019 Workshop <galaxy-sacnas-2019@lists.galaxyproject.org>; Mo Heydarian <mheydarian@gmail.com> Subject: [galaxy-sacnas-2019] Re: Next Wednesday! Genomic data science with the Galaxy workbench @ SACNAS Hello all, We have just 3 days to go! Some updates: Laptop In addition to Chrome or Firefox, please also install RStudio Desktiop<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Frstudio.com%2Fproducts%2Frstudio%2Fdownload%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615222235&sdata=wH771xXKtVUdruRLRWsvKeKEnQBwxyrf0zfc5qebjwo%3D&reserved=0>. Thanks to Ben Clarke for pointing this omission out. Code of Conduct SACNAS has a code of conduct<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.2019sacnas.org%2Fcode-of-conduct%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615232230&sdata=Qd1XUdVDBomDKjVVcVy0V3SfquNGEfHBk%2F1E5%2BsVgH8%3D&reserved=0>. Please review and abide by it. We have a cancellation to fill We have had two last minute cancellations. We have managed to fill one of them (Comet, welcome aboard, and please let me know if you get this email). However, we need help filling that last slot. If you know anyone who will be in Honolulu on Wednesday and would benefit from this workshop, then please let Mo and I know as soon as possible. See you Wednesday, Dave C On Thu, Oct 24, 2019 at 1:06 PM Dave Clements <clementsgalaxy@gmail.com<mailto:clementsgalaxy@gmail.com>> wrote: Hello All, We have less than a week to go before the Genomic data science with the Galaxy workbench<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgalaxyproject.org%2Fevents%2F2019-sacnas&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615232230&sdata=Hp484nORkeEZzTt8bJDg0YKCkd1b56hZ%2FAKfnQMx9jk%3D&reserved=0> pre-conference workshop at SACNAS. The workshop will be held Wednesday, October 30, 9am- 6pm in room 318AB at the Hawai’l Convention Center. Breaks (but not lunch - sorry, we could not afford it) will be provided. Here’s what you need to know for next Wednesday. Laptop The workshop will be hands-on! Please bring a fully charged,* wifi-enabled laptop with Firefox or Chrome already installed on it. Cancellation? This workshop is full, but people still want to attend. Please let us know as soon as possible if you can no longer make it. We Switched Examples We have switched our example analysis to differential gene expression (DGE). DGE is about figuring out what genes are turned on when. We had originally proposed using a genome wide association study (GWAS) as the example problem. GWAS was new to us, and after having explored that space we have decided that GWAS is not yet ready for a workshop. So 1. Don’t worry if none of the details above mean anything to you. We need a sample problem to work on and we have switched to a better one. 2. However, if you are keen to learn more about GWAS, we would be happy to discuss it with you over breaks and during the rest of SACNAS. Communication! We have set up two channels for communication. 1. This mailing list. We’ll use it to send out information that needs to go to everyone. 2. A workshop chat channel on Gitter.im: https://gitter.im/galaxyproject/SACNAS-2019<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgitter.im%2Fgalaxyproject%2FSACNAS-2019&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615242226&sdata=ihYuFOB6vVijMk9%2FGpiH%2BUjrU5yEoOzTnxP3o1aLcWI%3D&reserved=0>. Please use this for chat. We’ll use this for communication (for example, links) during the workshop, and for any discussion that doesn’t need to go to everyone, right now. You are already a member of the mailing list. And you can already see everything posted on chat. However, if you want to post something to chat, you will need to login to Gitter with either your GitHub**, GitLab, or Twitter ID***. Please let us know if you have any questions, and we will see you on Gitter, and in Honolulu next week, Mo H and Dave C --- * We aren’t sure of the power situation yet. ** Why you should be on GitHub (or GitLab)! If you don’t already have a GitHub<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615242226&sdata=GQJbyLJUkM%2BMi0Pg4N1oUUXtyDaTUVzQU9OhHd%2FRmro%3D&reserved=0> (or GitLab) account then we strongly recommend getting one. Data science happens with Git<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgit-scm.com%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615252216&sdata=2712MMFJlOfRKl6VP%2BeLdWAJR4uf4LL2QMKOJTwvzDI%3D&reserved=0>, and GitHub is the most popular platform for using Git. You won’t need to understand Git to understand this workshop. *** Why you should be on Twitter We can’t speak to disciplines outside of life sciences, but for life sciences these two quotes reflect the importance of Twitter in these fields: * Twitter is one of the most important bioinformatics tools you can use. <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dnalc.org%2Fabout%2Fstaff%2Fwilliams.html&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615252216&sdata=JCxzJN4wvSZSOkUh0bEQEjBE89mW2rQuaTtCAQFskfU%3D&reserved=0> Jason Williams<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.dnalc.org%2Fabout%2Fstaff%2Fwilliams.html&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615252216&sdata=JCxzJN4wvSZSOkUh0bEQEjBE89mW2rQuaTtCAQFskfU%3D&reserved=0>, CSHL & CyVerse * Twitter is the world's largest lab meeting. Someone at PAG<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.intlpag.org%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615262212&sdata=N8d2bZL5tRGlwj48U47UzJReHfN4tBv5OwdhH5PDcEQ%3D&reserved=0>, several years ago -- https://galaxyproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgalaxyproject.org%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615262212&sdata=q13NRqpHG0cMqasHHTBttc%2B0MAfaG75cNUfc%2BIpaYeo%3D&reserved=0> -- https://galaxyproject.org/<https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgalaxyproject.org%2F&data=02%7C01%7C%7C63badb79be394ce256a008d75b648431%7C02d8ff38d7114e31a9156cb5cff788df%7C0%7C0%7C637078359615272206&sdata=olFkwvgJmOjYHw74%2FRmCt0xB5ouiE3%2Frlkt2YP4C4%2Bg%3D&reserved=0> CAUTION: This email originated outside of the Seattle Colleges’ email system. 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participants (2)
-
Dave Clements -
Robinson, Marla