From 3d523bd6fc477fcb6f5870d1d0f650627f519af6 Mon Sep 17 00:00:00 2001 From: Melanie Date: Fri, 17 Nov 2023 23:14:02 +0100 Subject: [PATCH] Put the dev pages to the actual story pages --- DevStory2.html | 1209 -------------------------------- DevStory3.html | 1459 -------------------------------------- VisualizingCells.html | 257 +++++++ index.html | 17 +- story1.html | 7 +- story2.html | 1119 ++++++++++++++++++++++++++---- story3.html | 1541 ++++++++++++++++++++++++++++++++++++----- 7 files changed, 2633 insertions(+), 2976 deletions(-) delete mode 100644 DevStory2.html delete mode 100644 DevStory3.html create mode 100644 VisualizingCells.html diff --git a/DevStory2.html b/DevStory2.html deleted file mode 100644 index b201c3b..0000000 --- a/DevStory2.html +++ /dev/null @@ -1,1209 +0,0 @@ - - - - - - - 2: Identity Crisis - - - - - - - - - - - - - - - - - - -
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- 0. Scrollytelling Elements and Effects! - 1. What Is An HRA? - 2. Get to Know Your Anatomical Structures! - 3. Learn about Visualizing Cells in the Human Body -
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- This is the story of two of them: Squiggy and CeCe. -
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On this week's episode: 

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Squiggy's Identity Crisis!

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In which our heroes take a ride on HuBMAP's ASCT+B Reporter, learn that "partonomy" has nothing to do with the science of partying, and are reminded why it's always important to read notes from your mother.

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TV narrator: In conclusion, the Human - Reference Atlas is a - comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. -
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TV narrator: With the HRA, everyone will be able to find the names and - locations of all their favorite cells! -
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Squiggy: Hey, CeCe? -
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CeCe: What is it, Squiggy? -
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Squiggy: Have you ever - wondered about the big questions? You know: Who - am I? Do I belong? What is my purpose? -
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CeCe: Sure, Squig. I think - everybody does. -
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Squiggy: But I have so many - questions, and I don't know any of the - answers. This identity crisis has me all bent out of shape! -
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CeCe: Whoa, Squiq! Don't burst - your membrane! -
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CeCe: If you'd been paying attention, you would know that we can use the - Human Reference Atlas to figure out what you are and where you belong! -
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CeCe: And I think I know just the perfect place to start! -
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Squiggy: Ahh! Who just turned out all the lights? -
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CeCe: Don't worry Squiggy, it's just a scene transition. -
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Squiggy: Oh, well, I am NOT a fan. -
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CeCe: This is the Human Reference Atlas's ASCT+B - Reporter! -
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Squiggy: What does it do? -
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CeCe: Well, it can help us solve your identity crisis! -
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CeCe: You see, the ASCT+B Reporter allows researchers - to explore anatomical - structures, cell types, and biomarkers that make up different organs. -
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CeCe: The data tables from which the Reporter gets its - information are - authored - and reviewed by experts in their field. -
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- - - - other - Created with Sketch. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Ciliated bronchial cell - - - - - - - - - - - CDHR3 - - - CDHR4 - - - DNAH12 - - - DYNLRB2 - - - FOXJ1 - - - RSPH - - - TUBB4D - - - - - Pair of lungs - - - - - Lung - - - - - Lobe of lung - - - - - Lobar bronchus - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CeCe: - - You see, Squig, the - ASCT+B Tables are - arranged as a partonomy. - Just as the "lungs" are part - of the larger "body" - category, our next stop, the - "lobe of the lung," is part of - the larger lung category. - - - - - - - CeCe: - - Now you've got it, - Squiggy! - - - - - - - CeCe: - - Next stop cell types! - These are the blue dots. Oh, - and look at this. We've - happened to arrive at the - most awesome cell type in - the human body: the ciliated - bronchial cell. - - - - - - - CeCe: - - We ciliated bronchial - cells are important for your - respiratory system to - function. Our hair-like cilia - sway back and forth to - move particle-containing - mucus out of the way. - - - - - - - CeCe: - - Yeah, I'm kind of big - deal among the respiratory - crowd! - - - - - - - - - - - - ciliated - bronchial - cell - - - - - - CeCe: - Those lines lead to - biomarkers, which are - indicators like lipids, - proteins, genes, or - metabolites that provide - scientists with valuable - information about cell types - in both healthy and diseased - states. - - - - - - - CeCe: - - Going from the - ciliated bronchial cell node, - we can see that - my cell type - - is characterized by these - seven biomarkers. - - - - - - - - Squiggy: - - I get it! So, where - we're headed next, the lobar - bronchus, is part of the lobe - of the lung. - - - - - - - - Squiggy: - - Hey, wait a minute - CeCe, aren't YOU a... - - - - - - - Squiggy: - - Wow, CeCe, I didn't - know you were so important! - - - - - - - Squiggy: - - Hey, CeCe, I - thought we were finished. - Why are there lines coming - out of this blue node? - - - - - - - Squiggy: - - Wait a minute, Ce - Ce, I just realized why they - call this a PARTonomy. - - - - - - Squiggy: - - Ohhh, I see what - you did there! - - - - - - - CeCe: - - Hey Squig, how - about we check out my - favorite organ: the lungs! - - - - - - - -
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Squiggy: Do you think I - have biomarkers that would help scientists identify what kind of cell type I am? -
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CeCe: You bet, Squig! - Scientists have many ways of detecting the presence of characteristic biomarkers. -
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CeCe: Unfortunately, those - are way too complicated to get into right now, so let me just look at that tag on your back. -
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Squiggy: Tag? What tag? -
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CeCe: Right here! -
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Squiggy: Ooooh! -
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Squiggy: But how will these help me find out what kind of cell I am? -
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CeCe: I'll show you. Ready to go on another journey, Squiggy? -
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Squiggy: Oh, CeCe, please... no more! Don't make me ride this crazy thing again. I haven't recovered from the last trip! -
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CeCe: Alright, alright. Don't pop your nucleus. I've got an idea. -
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CeCe: Maybe we could ask these people out here to help. -
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Squiggy: What people? -
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CeCe: Those nice people out there who have been scrolling along and reading our adventure. -
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CeCe: How about it readers? Want to help out our friend? -
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Squiggy: Oh, please say "yes!" -
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CeCe: Then head over to the Reporter to find out what kind of cell type our friend is. -
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What Is Squiggy's Cell Type?

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  • Head over to the ASCT+B reporter to find out.
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  • Remember, Squiggy's biomarkers are Keratin 5/6, Keratin 7, p60.
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  • Along with being characterized by those biomarkers, Squiggy is a type of cell that can be found hanging out in the large intestine (among other places throughout the body).
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  • Choosing only the large intestine ASCT+B table and starting from there will make your job a lot easier!
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- Show hint - If you're stuck, watch this video tutorial. -
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- Hey I know! Squiggy's cell type is ... -

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Sebocyte

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Epithelial Stem Cell

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- Squamous -

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- Subepithelial membrane -

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- External links - -
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- @ 2023 Human Atlas Design System at Indiana University -
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- 0. Scrollytelling Elements and Effects! - 1. What Is An HRA? - 2. Get to Know Your Anatomical Structures! - 3. Learn about Visualizing Cells in the Human Body -
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- This is the story of two of them: Squiggy and CeCe. -
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On this week's episode: 

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Something's NOT Registering!

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In which our heroes explore HuBMAP's Registration User Interface (RUI), rescue - a stray human tissue sample, and learn that, when it comes to anatomy, "in the ballpark" is not - an ideal unit of measurement. -

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CeCe: Well good morning, Squiggy! You look pretty happy for having just rolled - out of bed. -
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Squiggy: I'm in a great mood, CeCe! After all, in our last adventure, I discovered my cell type and - resolved my identity crisis. -
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CeCe: And it looks like you bought yourself a shirt. -
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Squiggy: Oh, wow, CeCe. Thanks for noticing! It's a good thing I wore it - today because it's getting pretty chilly in here. -
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CeCe: Oh, I do - NOT like seeing that! -
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CeCe: It's a kidney - tissue sample, Squig, separated from its home organ and all alone. -
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Squiggy: Ah, that's no big deal. We can just pick this - little guy up, and the next kidney we come across, we can just stick him in somewhere! -
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CeCe: No way, Squig!! Don't you know that when you're - trying to identify a tissue sample, it's all about location, location, location! -
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Squiggy: What do you mean? Just look at that kidney! It - looks the same all over. Just a big brown blob. -
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CeCe: Well, Squig, that "big - brown blob" contains a great deal of variation. -
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CeCe: Right kidneys are - different from left kidneys, men's kidneys are different from women's kidneys, and don't get me started - on how kidneys can vary in shape, size, and location from person to person. -
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CeCe: And don't forget that - each kidney contains a number of distinct anatomical structures. These smaller structures have different - roles to play and are made up of different kinds of tissues and cell types. -
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CeCe: However, two distinct - anatomical structures may be only millimeters apart. -
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Squiggy: So, wait a minute. Are you saying that just guessing where our - tissue goes may not be a great idea? -
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CeCe: Well, Squig, let's just say that guesstimating is not exactly what researchers - call "best practice." -
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Squiggy: Well, that sounds impossible. I'm going back to bed. -
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CeCe: It's not hard at all, Squiggy. In fact, there's a tool to make it really easy! -
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- - - - Group 56 - Created with Sketch. - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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CeCe: Researchers can register their tissue sample - data with the Registration User Interface tool in the Human Reference Atlas. -
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CeCe: It takes only about 5 minutes to learn how to - do it and an average of 2 minutes to register a tissue block. -
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CeCe: All we need to do is select the correct organ. -
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CeCe: Now, let's position this kidney just how we - want it by using these buttons up here. -
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CeCe: Or we can rotate it with a mouse or keypad. -
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CeCe: Now, we can type in the height, width, and - depth of our tissue block. -
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Squiggy: What's that? -
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CeCe: That's how our tissue block appears in the 3D - world of the Registration User Interface! -
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CeCe: Now we can use these sliders here to rotate - the 3D block and move it into the correct place in the kidney. -
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CeCe: Now this is the fun part. I'm going to need - your help, Squiggy! -
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CeCe: We just need to move this tissue block so that - it's in the same place on this model as it was on the actual organ. -
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Squiggy: Look at us, CeCe, we're registering tissue! -
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CeCe: Now this is kind of cool. Watch as we move into the space of the 3D model, we'll - see an example of what's known as "collision detection." -
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Squiggy: Collision!! Ahhh!!! CeCe, I knew your crazy adventures would be - the end of me! Oh, goodbye cruel world! -
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Squiggy: Oh. Well, that was not very dramatic. -
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CeCe: Nope, Squiggy. You supplied ALL the drama we needed. -
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CeCe: You see, what our block is "colliding" with are anatomical structures. The RUI is - just letting us know what our tissue sample is bumping up against as we move it through the organ. This - helps for both placement and identification. -
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Squiggy: Well, I see what's been registered already, but it - looks like more information is needed. -
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CeCe: That's right, Squig. The Human Reference Atlas - is always looking for more data. -
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CeCe: The more tissue that's registered, and the - more other researchers can benefit from your correctly identified data, the more complete our picture of - the human body becomes. -
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CeCe: And that's a very good thing for understanding - our body in health and disease! -
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CeCe: So click on this link to the Registration User - Interface and register your tissue data today! -
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Squiggy: And don't forget to spay and neuter your pets! -
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+ Scrollytelling Series + What is a Human Reference Atlas? + +
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Learn about ...

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Visualizing Cells in the Human Body

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HuBMAP lets us visualize healthy cells in the human body in ways the naked eye can't do on its + own. With a + mountain of data available to us, we can better understand the different roles these cells play in + keeping + everything running smoothly.

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Using data expertise we can break down each organ into anatomical structures, functional tissue units + (FTU), + and cell types. The purpose of the three classes is to locate where in the body the cells are by + identifying + the organ, its smallest tissue unit that performs a unique physiologic function multiple times, and the + cell + types within that unit. From these perspectives, we can freely view the healthy human at multiple + scales. +

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While some parts of the human body can be easily recognized, like the kidneys in the graphic above, many + of us have no idea what the tissues and cells that make up a kidney look like.

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The human reference atlas currently + allows us to examine in some detail some of these cells. For instance: the renal corpuscle in the + kidney.

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The Renal Corpuscle

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In simple terms, the renal corpuscle is located in the kidney and works to filter out toxins through + urine + and reabsorb necessary nutrients back into your body.

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Within this FTU, there are several cell types + that + depend on each other for it to function. The renal corpuscle is made up of even smaller parts like + podocytes. Which, in turn, contain NPHS1 genes.

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The Large Intestine

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As it did for the renal corpuscle, HuBMAP also gives us the ability to map the crypt Lieberkuhn Glad in the + large intestine in detail. There are several cell types that work together to allow this FTU to renew the + lining of the intestine and produce mucus.

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What you've just seen is a glimpse into the possibilities HuBMAP can create. Imagine how our + understanding of human cells would accelerate if we did this for the entire body. From the crazy scales + it can go to, to the in-depth analysis of each cell, the human reference atlas can heavily influence the + advancement of human health and prospective research while serving as a convenient reference tool.

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On that note, we invite you to check out Andreas Bueckle's VR Organ Gallery that will soon be available + on the app store. The program is designed to be user-friendly in order to observe cells in 3D.

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+ + + + + + + + + + + + + + + + + diff --git a/index.html b/index.html index 3912eff..4db5c93 100644 --- a/index.html +++ b/index.html @@ -47,10 +47,10 @@ 3. Learn about the Number of Cells in the Human Body -->
- Scrollytelling Series - What is a Human Reference Atlas? - + + 1. What Is An HRA? + 2. Get to Know Your Anatomical Structures! + 3. Learn about Visualizing Cells in the Human Body
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Our stories so far...

-
Get to Know Your Anatomical Structures!
+
Something's Not Registering
 diff --git a/story1.html b/story1.html index e1e302e..636b984 100644 --- a/story1.html +++ b/story1.html @@ -42,10 +42,9 @@
- Scrollytelling Series - What is a Human Reference Atlas? - + 1. What Is An HRA? + 2. Get to Know Your Anatomical Structures! + 3. Learn about Visualizing Cells in the Human Body
diff --git a/story2.html b/story2.html index 354db9f..43d327c 100644 --- a/story2.html +++ b/story2.html @@ -11,12 +11,18 @@ + + + + + + +
+ External links + +
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