Monthly Archives: July 2013

Response to Inquiry Regarding Data Science Open Notebook & Posted E-mail Correspondence

Good Afternoon Dr. Budden,

I imagine you receive e-mail notifications for new blog posts –

However I wanted to point out I’ve taken a moment to expand in the open notebook on the interesting question you’ve brought to my attention regarding the “appropriateness” of logging e-mail messages in the Data Science open notebook.

In particular, I have become interested in the scenario of a potential visitor to the notebooks.dataone.org site who, lacking context, grows confused by what appears to be personal e-mail correspondence.

A solution I considered may be to preface any e-mail correspondence I post to the notebook with a header or “editor’s note” that explains something along the lines that “the following content is posted as part of ongoing research effort concerning open notebook science,” perhaps with a link to the tag “Open Notebook Science” or original entry describing the Data Science Open Notebook concept .

I am of course open to other suggestions or guidelines. As an example – on reflection I have realized I really should avoid entitling lab notebook entries “May 29 Research Effort” – or something witty like “To Infinity and Beyond” – since it adds little value to the post. Even though my analog research notebook might have an title “May 29 Research Effort,” the open notebook format may necessitate more disciplined thinking for assigning titles.

In any case, here is a link to my most recent entry expanding on the problem as posed: “Open Notebook Science – is it a blog or not?”

https://notebooks.dataone.org/data-science/open-notebook-science-is-it-a-blog-or-not/

Thanks,

Tanner

Archiving Two .XLS Documents in Sharepoint

From: Dave Vieglais [redacted]
Sent: Monday, November 19, 2012 11:46 AM
To: Jessel, Tanner Monroe
Cc: Dave Vieglais; Mitchell, Chad Matthew
Subject: Re: Request for File – DataONE users

Hi Tanner, I have attached the file from 20111025 and a new version created today.

Please do forward any final results from your analysis so that it may be archived if appropriate.

thanks,
Dave V,

20121119_dataone_users.xls

20111025_dataone_users.xls

On 2012.11.19, at 10:26 , “Jessel, Tanner Monroe” <tjessel> wrote:

Hello Dave, I sent this message to your G-mail account.

I thought I should’ve cc’d to your ku.edu to cover all my bases – here’s the message below:

I’m a Masters candidate in Information Science at UT-Knoxville working as a GRA on the DataONE project with Dr. Tenopir.

I’m working on a research question regarding social networks and influence within the DataONE user community.

Poking around on the DataONE docs.dataone.org site, I found a document you’d created in October of 2011 that I believe will be helpful in exploring this topic.

It’s called “List of DataONE users and groups” and apparently was created using a python script.

The exact filename is 2011025_dataone_users.xls

I found this file under “Project Information” <https://docs.dataone.org/member-area/project-information> on the main navigation menu of the DataONE docs site.

The download URL for the document is located on this page: https://docs.dataone.org/member-area/project-information/d1_users.xls/view, along with this description:

This spreadsheet lists members of DataONE, their group memberships and mailing list memberships. It is generated by the python script located in subversion software/tools/trunk/listusers/listusers.py executed with the command: python listusers.py -x file_name

I’m interested in this file as a view of historic membership of the DataONE community, but I’m also interested in re-creating the file to reflect current membership on the docs.dataone.org site.

I’m working with Chad Mitchell, another Masters candidate and research assistant at
UT-Knoxville.

He has some experience with python and I’m curious as well – if it’s possible for you to share, we’d like to learn how to generate a new file reflecting current membership.

Is this something that we or someone on the Dev team would have access to?

Barring re-creating your methods, we’d appreciate if you could supply us with a 2012 version of the d1_users.xls file.

Thanks for any help,

Tanner

Tanner Jessel
Graduate Research Assistant:
Data Observation Network for Earth (DataONE)
www.dataone.org

Center for Information and Communication Studies
The University of Tennessee
Mail: 1345 Circle Park Drive, Suite 420
Physical: Hoskins 5, Room 5-H
865-974-7931 (voice)
865-974-7973 (fax)
tjessel@utk.edu

Request for File – DataONE users


From: Jessel, Tanner Monroe
Sent: Wednesday, November 14, 2012 6:22 PM
To: Dave Vieglais; Mitchell, Chad Matthew
Cc: Amber E Budden
Subject: Request for File – DataONE users

Hello Dave,

I’m a Masters candidate in Information Science at UT-Knoxville working as a GRA on the DataONE project with Dr. Tenopir.

I’m working on a research question regarding social networks and influence within the DataONE user community.

Poking around on the DataONE docs.dataone.org site, I found a document you’d created in October of 2011 that I believe will be helpful in exploring this topic.

It’s called “List of DataONE users and groups” and apparently was created using a python script.

The exact filename is 2011025_dataone_users.xls

I found this file under “Project Information” <https://docs.dataone.org/member-area/project-information> on the main navigation menu of the DataONE docs site.

The download URL for the document is located on this page: https://docs.dataone.org/member-area/project-information/d1_users.xls/view, along with this description:

This spreadsheet lists members of DataONE, their group memberships and mailing list memberships. It is generated by the python script located in subversion software/tools/trunk/listusers/listusers.py executed with the command: python listusers.py -x file_name

I’m interested in this file as a view of historic membership of the DataONE community, but I’m also interested in re-creating the file to reflect current membership on the docs.dataone.org site.

I’m working with Chad Mitchell, another Masters candidate and research assistant at
UT-Knoxville.

He has some experience with python and I’m curious as well – if it’s possible for you to share, we’d like to learn how to generate a new file reflecting current membership.

Is this something that we or someone on the Dev team would have access to?

Barring re-creating your methods, we’d appreciate if you could supply us with a 2012 version of the d1_users.xls file.

Thanks for any help,

Tanner

Tanner Jessel
Graduate Research Assistant:
Data Observation Network for Earth (DataONE)
http://www.dataone.org

Center for Information and Communication Studies
The University of Tennessee
Mail: 1345 Circle Park Drive, Suite 420
Physical: Hoskins 5, Room 5-H
865-974-7931 (voice)
865-974-7973 (fax)
tjessel@utk.edu

Comments from Amber Budden Concerning "Policy" for doc.dataone.org Access

Note: I am summarizing comments from Dr. Budden here. I am not posting verbatim. Pertinent details from message are presered in header only:

From: Amber E Budden
Sent: Wednesday, November 14, 2012 1:58 PM
To: Jessel, Tanner Monroe
Subject: Re: docs.dataone access

no official documentation on who has access and who does not
no real ‘policy’ per se but
recognition such a policy might be beneficial

general guidelines:
anyone doing work for us should have access to the site.

  • leadership team
  • employees
  • WG members
  • students
  • postdocs
  • interns
  • etc.

As of this correspondence, except for interns, people who transition out of DataONE do not have access taken away, according to Budden.

DataONE retains ability to control access to specific materials:

  • (sensitive) documents that are for the Leadership Team only.
  • “culture of open science” dissuades expanding to other folders
  • exception: Anyone can become a member of our DataONE Users Group (DUG); therefore, DUG members are not granted access to Working Group materials to prevent viewing “without any context.”
  • ple transition out of DataONE we have not been restricting their access, with the exception of interns.

Original Query Below:

On Tue, Nov 13, 2012 at 11:03 AM, Jessel, Tanner Monroe <tjessel> wrote:

Good afternoon Amber,

I’m working on a research question related to network analysis of the DataONE community.

Do you happen to know if documentation exists on the docs.dataone.org site pertaining to criteria for membership in the docs.dataone.org community?

The reason I’m asking you is I remembered you’d set up permissions for me on the site.

So, I’m assuming you’re the “gatekeeper” and would be the best person to ask about who is granted access.

Thanks for any help on this,

Tanner

docs.dataone access

From: Jessel, Tanner Monroe
Sent: Tuesday, November 13, 2012 2:03 PM
To: Amber E Budden
Subject: RE: docs.dataone access

Good afternoon Amber,

I’m working on a research question related to network analysis of the DataONE community.

Do you happen to know if documentation exists on the docs.dataone.org site pertaining to criteria for membership in the docs.dataone.org community?

The reason I’m asking you is I remembered you’d set up permissions for me on the site.

So, I’m assuming you’re the "gatekeeper" and would be the best person to ask about who is granted access.

Thanks for any help on this,

Tanner

document info

From: Jessel, Tanner Monroe
Sent: Tuesday, November 13, 2012 1:36 PM
To: Mitchell, Chad Matthew
Subject: RE: document info

Hi Chad,

I am still working on setting up my computer in Hoskins.

First thing will be to install Gephi,

Then install an OCR / text extraction tool to pull out names and convert to a spreadsheet from these docs.

There is also a tool that will pull out proper names from uploaded text – if you want to go that route. Kind of data mining.

The problem is it won’t distinguish between a proper name in a cited paper (from let’s imagine, someone who died already but is nonetheless influential like charles darwin).

We should talk about how to contact vieglass on getting the registered users from docs.dataone.org.

-Tanner

DataONE Sharepoint – E-Mailing Attachments to Sharepoint

From: Jessel, Tanner Monroe

Sent: Thursday, July 25, 2013 4:26 PM
To: Davis, Miriam
Subject: DataONE Sharepoint – E-Mailing Attachments to Sharepoint

Hi Dr. Davis,

I am interested in archiving attachments sent to me via e-mail into the DataONE SharePoint site.

I did some research and was able to enable the service by more or less following the instructions described here:

http://office.microsoft.com/en-us/windows-sharepoint-services-help/add-content-to-sites-by-sending-e-mail-HA010086730.aspx

I also described in detail what I did here:
https://notebooks.dataone.org/data-science/ons-email-to-sharepoint/

Essentially, forwarding an e-mail with attachment(s) to the e-mail address I set up, [redacted], deposits the attachment into a folder in the root directory (cics/dataone/) that is linked to my user name.

That means I have a "tjessel" folder where anything I e-mail to [redacted] is archived.

If you were to e-mail something, a "miriams" folder would be created.

There is an option to have a new folder created based on subject heading, but I thought that could get messy, and besides, I thought it’d be good to keep things organized by who created it.

Another key point that I figure you’ll be interested in is only people with access to the site can forward documents with attachments. This is important to prevent spam.

Here’s where I’ve run into a problem:

I want to move documents from my "tjessel" folder to the "Network Analysis" folder you created.

I was able to do one at a time by clicking the check box next to each document and clicking "move to."

I think this is a bottle-neck in my workflow though.

Do you happen to know if this is a permissions problem, or can you really only move one document at a time to another folder?

I thought if you did not know yourself, you might be able to pass my inquiry along.

Thanks for any help,

Tanner

Tanner Jessel
Graduate Research Assistant:
Data Observation Network for Earth (DataONE)
http://www.dataone.org

Center for Information and Communication Studies
The University of Tennessee
Mail: 1345 Circle Park Drive, Suite 420
865-974-7973 (fax)
tjessel@utk.edu

Participant list available on docs.dataone.org


Note: attachment "20111025_dataone_users.xls" redacted due to personally identifiable information.
Will load to secure UT Sharepoint site and provide link

From: Jessel, Tanner Monroe
Sent: Tuesday, November 13, 2012 1:30 PM
To: Mitchell, Chad Matthew
Subject: Participant list available on docs.dataone.org

Chad, I came across this today on docs.dataone.org
Generated Oct. 25 2011, I believe it is a list of "Registered members of the DataONE team"
What is the word document you have?
I think we should see if we can get Dave Vieglais to generate a newer version of this.

Contact:
[redacted personal e-mail address]

Also, there is a "social network" here:
https://docs.dataone.org/participants

List of DataONE users and groups by Dave Vieglais last modified Oct 25, 2011 06:41 PM This spreadsheet lists members of DataONE, their group memberships and mailing list memberships. It is generated by the python script located in subversion software/tools/trunk/listusers/listusers.py executed with the command: python listusers.py -x file_name
Supported by the U.S. National Science Foundation (Grant #OCI-0830944) as one of the initial DataNets, DataONE will ensure the preservation, access, use and reuse of multi-scale, multi-discipline, and multi-national science data via three primary cyberinfrastucture elements and a broad education and outreach program.
Here is the information on the award:
http://nsf.gov/awardsearch/showAward?AWD_ID=0830944

Discipline Classification Survey Instrument & Informed Consent

Hi Dr. Allard,

Here is an attempt at a survey instrument for discipline classification, two sections and 8 questions total.

Section I includes questions about role and work environment.

Questions 1 and 2 derived from Arsev’s PhD dissertation (8 primary subject disciplines; 11 work settings).

Question 3, current job titles, is synthesized from the actual job titles of 284 DataONE.org members’ linkedIN profiles "Job Title" section, that I aggregated and merged into 17 main classifications. I expect the list could be honed further; or expanded, I would love to use the U.S. Census Bureaus list of Job Titles but I think people would get frustrated finding their desired title out of so many options, then quit the survey.

Of the options I provided, I am concerned about "Director" and "Manager;" "Research Fellow" and "Post Doctoral Researcher" and "Research Associate / Assistant." Perhaps I don’t understand these well enough.

Question 4 and Question 5 are about total career and "in discipline" career.

Section II contains demographics – credentials and degrees first, plus year obtained, and finally age / gender.

"Education" and "Computer Science" include special degrees – Doctor of Education, Education Specialist, and Doctor of Engineering, respectively. I don’t know if you want these homogenized as "Doctorate" or not.

There is an "other" in case there is a problem where a respondent does not see what they expect.

Let me know what the next steps are and if you have any questions.

Thanks,

Tanner

DataONE_Discipline_Survey-Informed-Consent.docx

DataONE_Discipline_Survey-Instrument.docx

Test 3: Network Visualization with NESCENT GeoPhyloBuilder

Hi Chad,

FYI because it’s cool, and also because I want to note it for future possible use on the network visualization project.

https://www.nescent.org/wg_EvoViz/Main_Page

https://www.nescent.org/wg_EvoViz/GeoPhyloBuilder

-Tanner