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[[Category: Data carpentry]][[Category: Biodiversity informatics]] | {| class="wikitable" style="float:right; margin-left: 10px;" | ||
This wiki supports the Data Carpentry Workshop | ! colspan="2" style="background:#D58B28;width:200px;font-size:10pt" |Data Carpentry | ||
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| colspan="2" style="text-align:center;font-size:7pt" |<!--YOU CAN INSERT A NEW IMAGE FOR THE LOGO BETWEEN THE COLON AND THE PIPE--> [[Image:ReproducibleWorkflows.png|center|400px|Image:ReproducibleWorkflows.png]]<br /> | |||
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!colspan="2" style="background:#D58B28;text-align:center;font-size:9pt" | Quick Links for Data Carpentry | |||
|- | |||
|[https://www.idigbio.org/wiki/index.php/Data_Carpentry#Agenda Data Carpentry Agenda] | |||
|- | |||
|[https://www.idigbio.org/biblio?f%5bkeyword%5d=436 Data Carpentry Biblio Entries] | |||
|- | |||
|[https://www.idigbio.org/wiki/index.php/Data_Carpentry#Link_to_Workshop_Report Data Carpentry Report] | |||
|} | |||
[[Category:Workshop]][[Category: Data carpentry]][[Category: Biodiversity informatics]] | |||
This wiki supports the Data Carpentry Workshop held simultaneously at the University of Florida at iDigBio and AMNH on September 29-30, 2014. It is the first in a series of four biodiversity informatics workshops planned in the upcoming year (2014-2015) for iDigBio. The next workshop in this series is [https://www.idigbio.org/wiki/index.php/Data_Sharing_Data_Standards_and_Demystifying_the_IPT Data Sharing, Data Standards, and Demystifying the IPT] (January 13-14, 2015). | |||
== General Information == | == General Information == | ||
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http://datacarpentry.github.io/2014-09-29-iDigBio/ | http://datacarpentry.github.io/2014-09-29-iDigBio/ | ||
==About== | === Planning Team === | ||
[mailto:francois.michonneau@gmail.com François Michonneau] (FLMNH - iDigBio), Katja Seltmann (TTD-TCN, MNH), Matt Collins (ACIS - iDigBio), Dan Stoner (ACIS - iDigBio), [mailto:dpaul@fsu.edu Deborah Paul] (FSU - iDigBio), Tracy K. Teal (BEACON), Pam Soltis (FLMNH - iDigBio PI), Derek Masaki (USGS - BISON), Shari Ellis (iDigBio), Kevin Love (iDigBio), Mike Smorul (SESYNC), Juliet Pulliam (UF), Ming Tang (Tommy) (UF), and assistance from Nirav Merchant at iPlant. | |||
===About=== | |||
'''Instructors:''' François Michonneau (FLMNH - iDigBio), Tracy Teal (MSU - BEACON), Matt Collins (ACIS - iDigBio), Katja Seltmann (TTD-TCN, AMNH) | '''Instructors:''' François Michonneau (FLMNH - iDigBio), Tracy Teal (MSU - BEACON), Matt Collins (ACIS - iDigBio), Katja Seltmann (TTD-TCN, AMNH) | ||
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Tuition for the course is free, but prior registration is required for attending. You can register [https://www.idigbio.org/content/data-carpentry-workshop-idigbio here.] | Tuition for the course is free, but prior registration is required for attending. You can register [https://www.idigbio.org/content/data-carpentry-workshop-idigbio here.] | ||
==Workshop Evaluation== | ===Workshop Evaluation=== | ||
* link to pre-workshop survey | * link to pre-workshop survey | ||
* | * [http://www.idigbio.org/sites/default/files/workshop-presentations/data-carpentry-idigbio/DataCarpentrySeptember2014Evaluation.pdf Post Data Carpentry Workshop Survey Results] | ||
==Software Installation Details== | ===Software Installation Details=== | ||
Software needed for Data Carpentry Workshop at iDigBio | Software needed for Data Carpentry Workshop at iDigBio | ||
*[http://datacarpentry.github.io/2014-09-29-iDigBio/ Data Carpentry software installation instructions] | *[http://datacarpentry.github.io/2014-09-29-iDigBio/ Data Carpentry software installation instructions] | ||
*You must RSVP that the required software is installed, prior to the workshop. Instructors are available to help - see your email for their contact information. | |||
We | We use Adobe Connect extensively in this workshop. Please perform the systems test using the link below. Also, you will also need to install the '''Adobe Connect Add-In''' to participate in the workshop. | ||
*[http://idigbio.adobeconnect.com/common/help/en/support/meeting_test.htm Adobe Connect Systems Test] | *[http://idigbio.adobeconnect.com/common/help/en/support/meeting_test.htm Adobe Connect Systems Test] | ||
==Agenda== | ==Agenda== | ||
*[https://idigbio.adobeconnect.com/e4r9cm91cjg/event/login.html?campaign-id=dc2014pt1 AdobeConnect #datacarpentry Room] | *[https://idigbio.adobeconnect.com/e4r9cm91cjg/event/login.html?campaign-id=dc2014pt1 AdobeConnect #datacarpentry Room] | ||
*Pre-workshop meeting and dinner at Piesano's, 6 PM Sunday September 28th. [https://www.google.com/maps/preview?ll=29.652657,-82.338597&z=15&t=m&hl=en-US&gl=US&mapclient=embed&q=1250+W+University+Ave+Gainesville,+FL+32601 Piesano's] is at NW 13th St. and 1250 W. University Ave. in Gainesville. All welcome. | |||
*Pre-workshop meeting and dinner at Piesano's, 6 PM Sunday September 28th. [https://www.google.com/maps/preview?ll=29.652657,-82.338597&z=15&t=m&hl=en-US&gl=US&mapclient=embed&q=1250+W+University+Ave+Gainesville,+FL+32601 Piesano's] is at NW 13th St. and 1250 W. University Ave. in Gainesville. | |||
{| class="wikitable" style="width: 55%;" | {| class="wikitable" style="width: 55%;" | ||
!colspan="3"| Course Overview - Day 1 | !colspan="3"| Course Overview - Day 1 | ||
|- | |- | ||
|8:30- | |8:30-8:45 | ||
| Introductions / | | Introductions & Overview, [http://www.idigbio.org/sites/default/files/workshop-presentations/data-carpentry-idigbio/datacarpentryidigbio2014.pptx Data Carpentry: Making data science more efficient] | ||
| | | All, Deb Paul | ||
|- | |||
|8:45-9:00 | |||
|[https://www.idigbio.org/sites/default/files/workshop-presentations/data-carpentry-idigbio/iDigBioDataCarpentryPSoltis.pptx Linking Heterogeneous Data in Biodiversity Studies: the need for data carpentry] | |||
| Pam Soltis, iDigBio PI | |||
|- | |- | ||
|9:00-10:00 | |9:00-10:00 | ||
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|- | |- | ||
| style="background-color: #eee;" |12:00-1:30 | | style="background-color: #eee;" |12:00-1:30 | ||
| style="background-color: #eee;" | Lunch | | style="background-color: #eee;" | Lunch | ||
| style="background-color: #eee;" | | | style="background-color: #eee;" | | ||
|- | |- | ||
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==Link to Workshop Report== | ==Link to Workshop Report== | ||
[https://www.idigbio.org/content/data-carpentry-please-can-we-have-some-more Data Carpentry - Please can we have some more?!] | |||
==Logistics== | ==Logistics== | ||
*[ | *[[Media:DataCarpentry_logistics.pdf |Logistics & Hotel Information (for the out-of-towners)]] | ||
*[https://www.idigbio.org//sites/default/files/workshop-presentations/data-carpentry-idigbio/AreaRestaurants.doc Where to find food] | *[https://www.idigbio.org//sites/default/files/workshop-presentations/data-carpentry-idigbio/AreaRestaurants.doc Where to find food] | ||
*[https://www.idigbio.org/content/data-carpentry-workshop-idigbio Workshop Calendar Announcement] | *[https://www.idigbio.org/content/data-carpentry-workshop-idigbio Workshop Calendar Announcement] | ||
*[[Media:Datacarpentry-registrations-Sep9-web.pdf |Participant List]] | |||
==Adobe Connect Access== | ===Adobe Connect Access=== | ||
Adobe Connect will be used to provide access for a remote classroom at the American Museum of Natural History. Workshop participants will be encouraged to be logged in to the Adobe Connect room to facilitate sharing with this remote group: | Adobe Connect will be used to provide access for a remote classroom at the American Museum of Natural History. Workshop participants will be encouraged to be logged in to the Adobe Connect room to facilitate sharing with this remote group: | ||
Already registered and accepted? | Already registered and accepted? | ||
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==Presentation Documents and Links== | ==Presentation Documents and Links== | ||
Links to any presentations (like power points) here. | |||
*[http://www.idigbio.org/sites/default/files/workshop-presentations/data-carpentry-idigbio/datacarpentryidigbio2014.pptx Data Carpentry: Making data science more efficient] Presenter: Deb Paul, iDigBio | |||
*[https://www.idigbio.org/sites/default/files/workshop-presentations/data-carpentry-idigbio/iDigBioDataCarpentryPSoltis.pptx Linking Heterogeneous Data in Biodiversity Studies: the need for data carpentry] Presenter: Pam Soltis, iDigBio PI | |||
*[https://github.com/datacarpentry/2014-09-29-iDigBio GitHub repository for Data Carpentry Workshop at iDigBio] | *[https://github.com/datacarpentry/2014-09-29-iDigBio GitHub repository for Data Carpentry Workshop at iDigBio] | ||
*[https://datacarpentry.etherpad.mozilla.org/13 EtherPad for Data Carpentry at iDigBio: workshop notes] | *[https://datacarpentry.etherpad.mozilla.org/13 EtherPad for Data Carpentry at iDigBio: workshop notes] | ||
*[https://github.com/datacarpentry/2014-09-29-iDigBio/blob/master/cheatsheets/sql.pdf?raw=true SQL commands list] | |||
*[https://github.com/datacarpentry/2014-09-29-iDigBio/blob/master/cheatsheets/shell.pdf?raw=true SHELL commands list] | |||
*[http://datacarpentry.github.io/2014-09-29-iDigBio/lessons/R/ R lesson] | |||
*[http://openrefine.org/ Getting started with Open Refine] | |||
==Workshop Recordings== | ==Workshop Recordings== | ||
====Day 1==== | ====Day 1==== | ||
* | *8:30am-10:00am http://idigbio.adobeconnect.com/p7gqmvndl5a/ | ||
* | *10:30am-12:00pm http://idigbio.adobeconnect.com/p6ipl39xnl3/ | ||
* | *12-12:30 http://idigbio.adobeconnect.com/p4dsgo0y77y/ | ||
*1:00pm-5:00pm http://idigbio.adobeconnect.com/p4rm50ukzv5/ | |||
====Day2 ==== | ====Day2 ==== | ||
* | *8:30am-10:00am http://idigbio.adobeconnect.com/p2crpl68wr4/ | ||
* | *10:30am-12:00pm http://idigbio.adobeconnect.com/p1e150mot75/ | ||
* | *1:30pm-5:00pm http://idigbio.adobeconnect.com/p4t16mcnvvk/ | ||
==Data Carpentry Resources and Links== | ==Data Carpentry Resources and Links== | ||
*[https://github.com/datacarpentry/2014-09-29-iDigBio Data Carpentry Materials on GitHub] | *[https://github.com/datacarpentry/2014-09-29-iDigBio Data Carpentry Materials on GitHub] | ||
*[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003542 Ten Simple Rules for the Care and Feeding of Scientific Data. Goodman et al] | *[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003542 Ten Simple Rules for the Care and Feeding of Scientific Data. Goodman et al] | ||
*[http://faculty.chicagobooth.edu/matthew.gentzkow/research/CodeAndData.pdf Code and Data for the Social Sciences: A Practitioner's Guide. Matthew Gentzkow, Jesse M. Shapiro Chicago Booth and NBER March 10,2014] | *[http://faculty.chicagobooth.edu/matthew.gentzkow/research/CodeAndData.pdf Code and Data for the Social Sciences: A Practitioner's Guide. Matthew Gentzkow, Jesse M. Shapiro Chicago Booth and NBER March 10,2014] | ||
*[http://dx.doi.org/10.4033/iee.2013.6b.6.f Nine simple ways to make it easier to (re)use your data. White et al.] | *[http://dx.doi.org/10.4033/iee.2013.6b.6.f Nine simple ways to make it easier to (re)use your data. White et al.] | ||
*You want to learn SQL independently? Try [http://www.headfirstlabs.com/books/hfsql/ Head First SQL] | |||
*[http://shop.oreilly.com/product/9780596807702.do Head First Excel, O'Reilly] | |||
*Check out [https://www.dataone.org/ DataONE] | |||
**They've got a great [https://www.dataone.org/software_tools_catalog Software Tools Catalog] | |||
*Put standard metatdata with your data. Wondering how to do that? Check out DataONE's Morpho Tool available under the tools menu at https://knb.ecoinformatics.org/. | |||
**Why? Makes your data re-useable, and better still, makes your data discoverable. Get cited for your datasets in addition to your published papers! | |||
*Using Open Refine? Want to compare your taxon names against a standard list? Try this reconciliation service. | |||
**Read Gaurav ' Blog post first: http://gbif.blogspot.com/2013/07/validating-scientific-names-with.html | |||
**Then, give it a try. The google plus Open Refine community will help you figure it out (it's not hard). | |||
===Links from You=== | |||
*How about you? Got a favorite resource - a book?, a website? to share with your classmates? | |||
*[http://datascienceatthecommandline.com/ Data Science at the Command Line] | |||
*[http://www.it.ufl.edu/training/ Free Training Resources for UF students, faculty, and staff] UF provides free access to over 2600 online training courses through Lynda.com. Does your institution have similar free training opportunities? | |||
===Related Blog Posts and Photos=== | |||
*[http://nescent.github.io/2014-05-08-datacarpentry/ Inaugural Data Carpentry Workshop] by Tracy K. Teal | |||
*[http://software-carpentry.org/blog/2014/05/our-first-data-carpentry-workshop.html Our First Data Carpentry Workshop] by Karen Cranston | |||
*[https://www.idigbio.org/content/tales-data-carpentry-workshop-demand Tales from the First Data Carpentry Workshop] by Deb Paul, May 2014 | |||
*[https://www.idigbio.org/content/data-carpentry-please-can-we-have-some-more Data Carpentry, Please can we have some more?!] by Deb Paul, 15 Oct 2014 | |||
*[https://www.facebook.com/media/set/?set=a.790950270948921.1073741844.215120891865198&type=3 Data Carpentry Facebook Photo Album] | |||
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