Updated Open Science presentation by knoll-alex · Pull Request #2 · knoll-alex/samirdas.github.io

knoll-alex · 2019-10-02T21:49:46Z

No description provided.

*Unneeded slides

christinerogers

Nice! All good stuff.
I've noted a few refinements to make -- better links to use, places to remove links.
Please see my requests in-line. 👍

Please also do: add the file extension .html to this file

i didn't actually look at the presentation from the front-end yet - how it looks/presents/works, i just read your code changes :)

christinerogers · 2019-10-04T18:12:26Z

Open_Science_New

-	    <h2><Demo</h2>
-		   <img src="images/Open_science_paper.png">
+	    <h2>Demo</h2>
+		   <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5216036/"><img src="images/Open_science_paper.png"></a>


This is the link to the actual paper that NIH page points to :
https://www.frontiersin.org/articles/10.3389/fninf.2016.00053/full

thanks, done!

christinerogers · 2019-10-04T18:15:44Z

Open_Science_New

-		  <img src="images/Nidm.png">
-		  <img src="images/BIDS.png">
+		  <a href="http://nidm.nidash.org/specs/nidm-overview.html"><img src="images/Nidm.png"></a>
+		  <a href="https://bids.neuroimaging.io"><img src="images/BIDS.png"></a>


Add the brand new BIDS logo where you can, it was just released in June.

black version is found on their wikipedia page

white version should be downloadable from https://bids.neuroimaging.io/

christinerogers · 2019-10-04T18:18:03Z

Open_Science_New

 	      <tr>
 		<td width="75%" style="vertical-align: middle">
-		  <img src="images/C-BASE.png">
+		  <a href="http://www.digitalinberlin.de/c-base/"><img src="images/C-BASE.png"></a>


let's remove this link. That pic was just the uber-cool venue for one particular hackathon in 2014, no need to point people to it.

christinerogers · 2019-10-04T18:19:34Z

Open_Science_New

 	  <!-- Our implementation -->
 	  <section>
-	    <section data-background="images/mni_eco_info_5.jpg" data-background-size="100%">
+	    <a href="https://samirdas.github.io/MNI_ecosystem.html#/"><img src="images/mni_eco_info_5.jpg" data-background-size="100%"></a>


Make a note/bookmark -- we will probably want to come back and update this link later, given it points to a presentation that should also get revamped soon.

christinerogers · 2019-10-04T18:21:58Z

Open_Science_New

 		  </td>
 		  <td>
-		    <img src="images/LORIS_paper.png"> 
+		    <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3262165/"><img src="images/LORIS_paper.png"></a>


this paper is hosted on our Loris.ca site. use the URL there (so that people without academic access can always download it) :
http://loris.ca/images/LORIS-paper-frontiers.pdf

thanks, done

christinerogers · 2019-10-04T18:24:09Z

Open_Science_New

 	  <!-- Cuban Brain Mapping -->
 	  <section data-transition="convex">
-	    <a href="" target="_blank"><img src="images/Cuban_brain_mapping.png" width="120%"></a>
+	    <a href="https://journals.sagepub.com/doi/abs/10.1177/155005941104200303?rfr_dat=cr_pub%3Dpubmed&url_ver=Z39.88-2003&rfr_id=ori%3Arid%3Acrossref.org&journalCode=eegb"><img src="images/Cuban_brain_mapping.png" width="120%"></a>


the URL is :
https://doi.org/10.1177/155005941104200303
Pro tip: always use a DOI link if you can for almost anything

thanks! this was removed so N/A

christinerogers · 2019-10-04T18:25:30Z

Open_Science_New

 	      <tr>
 		<td width="45%" style="vertical-align: middle">
-		  <img src="images/ABIDE_paper.png">
+		  <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4162310/"><img src="images/ABIDE_paper.png"></a>


the actual paper is here:
https://dx.doi.org/10.1038%2Fmp.2013.78

thanks! this was removed so N/A

christinerogers · 2019-10-09T15:25:20Z

Open_Science_New.html

+          <!-- OHBM Column 6-->
+              <section>
+                  <section>
+              <h3>Organization for Human Brain Mapping (OHBM) Iniatives</h3>


Please update as follows:

OHBM as top header

"Organization ...." as secondary heading, smaller font.

Done - paired down the explanation as well, and took out the italics

Open_Science_New.html

knoll-alex · 2019-10-10T19:24:11Z

Open_Science_New.html

+
+		  <td width="50%" style="vertical-align: middle;">
+		    <a href="https://www.scienceeurope.org/" target="_blank"><img src="images/ScienceEurope.png" style="border:0; border-radius:30px;"></a>
+		    <p><small><br>This intiative was officially launched as<br>


@christinerogers Found this info through my research - is it accurate and relevant?

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/1/6

Good question. it's accurate but not relevant --
i'm not 100% sure what the scope of "this info" refers to but let's remove Science Europe... "Plan S" Brussels-based... since we don't engage with them or have connections to it

knoll-alex · 2019-10-10T19:39:05Z

Open_Science_New.html

+   	<section>
+	  <h2><font color="12a3d8">What’s involved?</font></h2>
+	  <p>
+	    Longitudinal Acquisition, Storage and Curation, <font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, Security, Privacy, Ethics, APIs, Validation, Quality Control, Protocol Checking, Preprocessing, Analysis, HPC, Provenance, Ontological Standarization,<br><font color="f27c30">Data Harmonization</font>, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, <font color="f27c30">Extensibility</font>, Data Management, Summary Statistics, Workflows, Development, Tool Integration, <font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR <font color="f27c30">...No big deal!</font>


@christinerogers couldn’t quite figure out how to properly make this into an unordered list that fits on the page - should we just keep it like this? I don't think it looks too bad, and the orange font helps quickly display which features and most prominent/important

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/1/9

Hmm, it would be nice to have the terms be more legible, (like in a word cloud) even if not in an ordered list.
Let's try a few minimal changes:

add 4-7 spaces to replace every comma, to separate terms (whatever ends up looking best)

add line breaks assuming a 13" monitor? because some terms are getting separated (e.g. bug fixes)

@christine - I tried this and I found it looked worse. I'm thinking it's fine to leave it as is? People are either going to be interested in reading every word or not. The orange helps highlight the most important ones. I'm not sure formatting this differently would help any further

knoll-alex · 2019-10-10T19:39:36Z

Open_Science_New.html

+
+          <!-- Open Science Initiatives - Column 2 -->
+    <section data-transition="convex">
 	    <h2>Open Science Initiatives</h2>


@christinerogers there's text hidden below these images that doesn't fit on the page - do you know a fix?

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/2

knoll-alex · 2019-10-10T19:40:07Z

Open_Science_New.html

+              <!-- MNI Open Science CyberInfrastructure -->
+	  <section>
+		   <a href="https://www.frontiersin.org/articles/10.3389/fninf.2016.00053/full"><img src="images/Open_science_paper.png" width="75%" height="75%"></a>
+          <p><small>MNI's LORIS and CBRAIN platforms (more on these later) have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing.</small></p>


@christinerogers suggestions on improved wording for this blurb?

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/3/2

knoll-alex · 2019-10-10T19:40:41Z

Open_Science_New.html

+                      <p>Healthy Brains, Healthy Lives</p>
+              <a href="https://www.mcgill.ca/hbhl/"><img src="images/hbhl_logo.png"></a>
+              <p><small><i>Exploring our brains' role in health and disease throughout our lives.</i></small></p>
+              </section>


@christinerogers Are there any additional slides to include for HBHL? it seems lonely

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/4

I looked up the "About HBHL" page from the website.
How about this copy?

A high-priority trans-disciplinary initiative focussing on areas of neuroscience that hold the greatest promise for delivering implementable, clinically effective outcomes in brain and mental health.
Supported by Canada First Research Excellence Fund (CFREF) and based at McGill University.
Scientific Director: Alan Evans.

knoll-alex · 2019-10-10T19:41:29Z

Open_Science_New.html

-	<section>
-
-	  <!-- Interoperability -->
+           <!-- Interoperability Column 7-->


@christinerogers Not too familiar with most of these slides (lines 272-350, columns 7 and 8) so I just want to make sure that they are all relevant and necessary and up-to-date

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/7

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/8

Sure, i just took a look. let's try :

yellow strikes me as inconsistent with the rest of the deck. Would the orange used previously work better?

add a one-line plain-language synopsis for each of interoperability/standardization e.g. :

(interoperability) Systems should allow the exchange of data in standardized ways

(standardization) compatibility across data definitions and formats

knoll-alex · 2019-10-10T19:42:45Z

Open_Science_New.html

-	    <img src="images/Datalad.png">
-	  </section>
+	  <!-- Git -->
+              <section>


@christinerogers Another issue with fitting on one page - do you know a solution? Also to remove that weird border line? I consolidated all the git slides into this one slide so if there's no way to make it fit we can just re-separate them.

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/9/4

try downsizing the images, or else just use their logos.

subtitle for this slide: Open tools for streamlining workflows and storing code, datasets and more

knoll-alex · 2019-10-10T19:43:12Z

Open_Science_New.html

+             <table class="reveal">
+		<tr>
+		  <td width="50%" style="vertical-align: middle">
+		    <ul><li>A systematic way of recording data</li>


@christinerogers Are these bullet points accurate? I wasn't sure how to refine them.

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/10

let's try an edit with fewer words:

standardized Consent codes

based on global genomic standards

knoll-alex · 2019-10-10T19:44:02Z

Open_Science_New.html

 		    <img src="images/Data_breach_consent.png">
-		    <img src="images/Data_breach.png">
-		    
+		    <img src="images/Data_breach.png"></a>


@christinerogers Another fitting issue :( Also - do I need to add contextual text here? the articles and headlines seem self-explanatory

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/10/1

i agree, self-explanatory.
let me know how re-sizing the image widths goes

knoll-alex · 2019-10-10T19:44:18Z

Open_Science_New.html

 	    </section>
-
-	    <section>
+            <section>


@christinerogers not fitting on page

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/11/1

christinerogers · 2019-10-10T19:47:25Z

Open_Science_New.html

-	  </section>
+		<a href="https://www.sciencemag.org/news/2016/01/montreal-institute-going-open-accelerate-science"><img src="images/Open_science.png"></a>
+	    </td></tr></table>
+        <p><small>In the following columns, we'll look at some current initiatives.</small></p>


why "columns" ?

@knoll-alex let's try: replace "In the following columns," with "Next,"

christinerogers

Hi Alex, next round of feedback -- I hope I got to all your questions in this.
I also noticed some further update/streamline opportunities.

some of my requests here contradict previous - e.g. now that I'm previewing I can see that adding the spelled-out subheader for OHBM was superfluous, given the logo!

christinerogers · 2019-10-24T22:00:21Z

Open_Science_New.html

+
+		  <td width="50%" style="vertical-align: middle;">
+		    <a href="https://www.scienceeurope.org/" target="_blank"><img src="images/ScienceEurope.png" style="border:0; border-radius:30px;"></a>
+		    <p><small><br>This intiative was officially launched as<br>


Good question. it's accurate but not relevant --
i'm not 100% sure what the scope of "this info" refers to but let's remove Science Europe... "Plan S" Brussels-based... since we don't engage with them or have connections to it

christinerogers · 2019-10-24T22:04:34Z

Open_Science_New.html

+   	<section>
+	  <h2><font color="12a3d8">What’s involved?</font></h2>
+	  <p>
+	    Longitudinal Acquisition, Storage and Curation, <font color="f27c30">Interoperability, Reproducibility</font>, Transfer, Anonymization, Security, Privacy, Ethics, APIs, Validation, Quality Control, Protocol Checking, Preprocessing, Analysis, HPC, Provenance, Ontological Standarization,<br><font color="f27c30">Data Harmonization</font>, Upgrades, Maintenance, Bug Fixes, User Interface, Javascript, Bootstrap, Tracking, <font color="f27c30">Extensibility</font>, Data Management, Summary Statistics, Workflows, Development, Tool Integration, <font color="f27c30">Data Sharing</font>, Download, Multi-Modal Linking, <font color="f27c30">Querying</font>, Image Processing, Visualization, Networking, System Administration, Partnerships, Funding, HR <font color="f27c30">...No big deal!</font>


Hmm, it would be nice to have the terms be more legible, (like in a word cloud) even if not in an ordered list.
Let's try a few minimal changes:

add 4-7 spaces to replace every comma, to separate terms (whatever ends up looking best)

add line breaks assuming a 13" monitor? because some terms are getting separated (e.g. bug fixes)

@christine - I tried this and I found it looked worse. I'm thinking it's fine to leave it as is? People are either going to be interested in reading every word or not. The orange helps highlight the most important ones. I'm not sure formatting this differently would help any further

christinerogers · 2019-10-24T22:15:00Z

Open_Science_New.html

-	  </section>
+		<a href="https://www.sciencemag.org/news/2016/01/montreal-institute-going-open-accelerate-science"><img src="images/Open_science.png"></a>
+	    </td></tr></table>
+        <p><small>In the following columns, we'll look at some current initiatives.</small></p>


@knoll-alex let's try: replace "In the following columns," with "Next,"

christinerogers · 2019-10-24T22:19:34Z

Open_Science_New.html

+              <!-- MNI Open Science CyberInfrastructure -->
+	  <section>
+		   <a href="https://www.frontiersin.org/articles/10.3389/fninf.2016.00053/full"><img src="images/Open_science_paper.png" width="75%" height="75%"></a>
+          <p><small>MNI's LORIS and CBRAIN platforms (more on these later) have been tasked with the technical challenges specific to the institutional-level implementation of open data sharing.</small></p>


change MNI to MCIN (we kinda want the credit)

for have been tasked... let's try: have demonstrated the technical capacity to address the challenges of open science at an institutional level

christinerogers · 2019-10-24T22:20:53Z

Open_Science_New.html

-	    <p><font color="yellow">It's the future!</font></p>
-	    <a href="https://www.youtube.com/watch?v=Wtp7R97jz5k" target="_blank"><p><small><font color="orange">Aled Edwards video</font></small></p></a>
+	    <a href="https://samirdas.github.io/MNI_ecosystem.html#/"><img src="images/mni_eco_info_5.jpg" data-background-size="100%"></a>
+          <p><small>View this presentation (click image to open) for further details


how about:Click to View this presentation in a new tab

(also pls make sure it opens in a new tab)

christinerogers · 2019-10-24T23:05:48Z

Open_Science_New.html

@@ -438,28 +478,30 @@ <h2>Extensible and modular design</h2>
            <img src="images/EEG.png">


slide title: "Multi-modal and BIDS-compliant features"

christinerogers · 2019-10-24T23:06:49Z

Open_Science_New.html

+
+        <section>
+            <section>
+              <a href="CBRAIN_indepth.html#/cbrain-indepth-destination" target="_blank"><h2>Introducing... CBRAIN!</h2></a>


again... revert, thanks :)

christinerogers · 2019-10-24T23:09:35Z

Open_Science_New.html

+	</tr></table>
 	    </section>

 	     <section>


NOTE @knoll-alex see how this CBRAIN slide answers "Where are we" and "who uses us" ?
It would be good to mirror this info progression roughly in the first few LORIS slides (for this, use the info in the linked google slides in my comment in that section)

christinerogers · 2019-10-24T23:11:24Z

Open_Science_New.html

-		<td width="55%" style="vertical-align: middle">
-		  <img src="images/ABIDE_preprocessed.png">
+		<td width="25%" style="vertical-align: middle">
+		  <p> Important value of hackathons to data sharing initiatives</p>


instead
Vital environments for collaboration and exchange of ideas, tools and solutions for data sharing initiatives

it looks too narrowly constricted - try the width

christinerogers · 2019-10-24T23:13:31Z

Open_Science_New.html

+<!-- Acknowledgemnts-->
 	<section data-transition="slide" data-background="#87CEEB" data-background-transition="zoom">
 	  <table class="reveal">
 	    <tr>


update the team grid with the 2018 version here:
http://lorisdb.github.io/about.html

update: we'll have a new version up on loris.ca later this week...

knoll-alex · 2019-10-31T01:11:15Z

Thanks @christinerogers - made a bunch of changes per your comments

knoll-alex · 2019-10-10T20:15:54Z

Open_Science_New.html

+
+          <!-- Infrastructure Column 9-->
+          <section>
+              <section data-transition="fade" data-background="images/infrastructure.png">


Any idea why this image isn't showing up?

https://htmlpreview.github.io/?https://github.com/knoll-alex/samirdas.github.io/blob/ak-Open_Science/Open_Science_New.html#/9

@christinerogers The image still isn't showing up :(

knoll-alex · 2019-11-05T16:48:58Z

Open_Science_New.html

-	  
+
 	  <section>
 	    <h2>File Formats</h2>


@christinerogers I can't figure out why this image isn't showing up! It's in the images folder and the file is named correctly here.

knoll-alex added 3 commits October 2, 2019 17:49

Added hyperlinks to all relevant images

8ad7e1e

Added more links to images

d9bf95d

Added more image links and removed slides*

5f0addc

*Unneeded slides

christinerogers suggested changes Oct 4, 2019

View reviewed changes

knoll-alex added 4 commits October 7, 2019 14:03

Renamed to include html

9cde595

Update Open_Science_New.html

30496db

Final version ready for Oct 9 call

80739e3

Added images for Open_Science pres

18c4e01

knoll-alex changed the title ~~Added hyperlinks to all relevant images~~ Updated Open Science presentation Oct 9, 2019

christinerogers reviewed Oct 9, 2019

View reviewed changes

knoll-alex commented Oct 9, 2019

View reviewed changes

Open_Science_New.html Outdated Show resolved Hide resolved

Updated with changes after Oct 9 call

87e7dfe

knoll-alex commented Oct 10, 2019

View reviewed changes

christinerogers reviewed Oct 10, 2019

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christinerogers suggested changes Oct 24, 2019

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christinerogers mentioned this pull request Oct 30, 2019

AK_Open_Science_New samirdas/samirdas.github.io#8

Open

knoll-alex added 4 commits October 30, 2019 21:12

More changes per Christine's comments

c08816b

Update Open_Science_New.html

cba6ba3

photos for open science

a4d05ca

Add files via upload

7a9e98d

knoll-alex added 3 commits October 30, 2019 21:23

Add files via upload

db16894

Add files via upload

b45d699

Update Open_Science_New.html

397adfd

knoll-alex commented Nov 5, 2019

View reviewed changes

		@@ -438,28 +478,30 @@ <h2>Extensible and modular design</h2>
		<img src="images/EEG.png">

Conversation

knoll-alex commented Oct 2, 2019

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