CCST9064-Video-Essay
File description: The final video essay submitted for CCST9064 group project. Python code for Manim included.
Document status: UNK
Last modified: 2026-09-11 21:12 HKT
This is a collection of resources for the CCST9064 video essay submission. There are three parts in this collection:
-
The video: The final video essay submitted by the group. Available on YouTube.
-
The Python source code: The Python code used for creating Manim animations in the video essay.
-
The video project file: The original Adobe Premiere Pro project file used for editing the video essay.
-
The individual research log: The individual research log submitted by each group member.
Video
The final video is uploaded to YouTube. The video is unlisted, but you may access it via the button above, or view it below:
If the video is not displayed properly, please use the button above to view on YouTube.
HDR Content
This video was created in HDR (High Dynamic Range) format. If your display does not support HDR, the colours may appear washed out or less vibrant on your screen.
Python Source Code
The video uses extensive Manim animations. The Python source code used to create these animations is available as an archive file.
Python 3.12 was used during development. Lower versions may work but are not tested. Please ensure that you have the required dependencies installed.
To build the animations, do:
pip install -r requirements.txt # Install dependencies
manim -qh [SCRIPT_NAME] # Render the animation in high quality,
# follow the interactive instructions from Manim.
Video Project File
The original Adobe Premiere Pro project file, along with all the footages, assets, Adobe After Effects project files, are packed into an archive for download. You will need Adobe Premiere Pro 2025 and Adobe After Effects 2025 to open and edit the project. As the archive is large, you will be redirected to Google Drive for downloading.
Individual Research Log
An individual research log is submitted separately via Moodle. You can also download the research log using the button above. Below is a preview of the research log:
CCST9064 Group L { Video Essay
Individual Research Log
Student Information
Name:
SHING, Zhan Ho Jacob
Student ID:
3036228892
Group Number:
L
Topic:
Somatic Gene Therapy
1 Research Approach and Methodology
For this group project, I am not responsible for the research part. However, for video production purposes,
research was still an essential part to obtain contents and ensure my content's accuracy.
The sources that I have consulted, as will be listed in the later sections, are mainly from credible scientic
database { the Protein Data Bank (PDB) { and educational videos from reputable channels on YouTube. The
research methodology mainly involves keyword searching within PDB and YouTube. The keywords are taken
from the video script written by the scriptwriters and from the storyboard.
2 Key Sources Consulted
As our video essay is about highly specialised scientic topic { somatic gene therapy { there are many credible
sources that can be used to explain the concepts clearly visually. Using existing materials also saves the
production time and reduces the need for creating complicated animations
de novo
. I have researched and
collected the following materials:
2.1 3D Models of Protein Structures
Many of the protein structures are already determined through experimental methods and are available in the
Protein Data Bank (PDB,
https://www.rcsb.org/
). Further, for dynamically showing the structures, the
molecular data downloaded from PDB can be fed into the software ChimeraX (
https://www.cgl.ucsf.edu/
chimerax/
), colour-coded, and exported as a 3D object le, that can be further animated with After Eects.
In our video essay, the following protein structures were (adapted and) used:
[1APL]
Crystal Structure of a MAT-
2 Homeodomain-Operator Complex Suggests a General Model for
Homeodomain-DNA Interactions
{ the double helix DNA structure was extracted for the opening scene.
[2HHB]
The Crystal Structure of Human Deoxyhaemoglobin at 1.74 Angstroms Resolution
{ the normal
human haemoglobin structure, used along with
2HBS
.
[2HBS]
The High Resolution Crystal Structure of Deoxyhemoglobin S
{ the sickle-cell haemoglobin
structure, used along with
2HHB
to illustrate the molecular basis of sickle-cell anaemia.
[3FSN]
Crystal Structure of RPE65 at 2.14 Angstrom Resolution
{ to illustrate the protein involved in
gene therapy for Leber's Congenital Amaurosis (LCA).
[4QQ6]
Crystal Structure of tudor domain of SMN1 in complex with a small organic molecule
{ to
illustrate the protein involved in gene therapy for Spinal Muscular Atrophy (SMA).
Apart from the models provided by PDB, there was also one double helix DNA model created by the software
ChimeraX, using a randomly generated DNA sequence, for animating the rotating double helix DNA in the
video.
2.2 Video/Animation Clips
To illustrate the complex biological processes involved in somatic gene therapy, I have searched for existing
video/animation clips that can be used directly or adapted for our video essay. The following clips were used:
3D Animation of a Clogged Blood Vessel Due to a Sickle Cell Disease
(
https://youtu.be/BmnfR-D8ewE
)
{ to illustrate the eect of sickle-cell anaemia blocking blood vessels.
Gene Therapy Basics (2022 Update)
(
https://www.youtube.com/watch?v=kAtd9X29SdQ
) { to illustrate
\delivering a healthy gene into a cell as compensation".
1
Page 1 of 30
Breast Cancer
(
https://vimeo.com/871843858
) { to illustrate the idea of uncontrolled cell growth in
cancer.
Introduction to CRISPR-Cas9 Genome Editing
(
https://www.youtube.com/watch?v=iEA-NleJoqY
) {
to illustrate the CRISPR-Cas9 gene editing mechanism.
A Look at How CAR-T Cell Therapy Works
(
https://www.youtube.com/watch?v=mXADrg_ckhI
) { to
illustrate the CAR-T cell therapy mechanism.
3 Major Insights and Discovery
As opposed to my original expectation that all of the protein structures in our body can be found on PDB
as long as their genetic sequences are known, during the research process, I have discovered this to be false.
Many of the protein structures cannot be found on PDB. Later investigations on this issue revealed that the
structure of a protein cannot be determined simply through mathematical or computer simulations even if the
exact amino acid chain is known. This is because protein folding is a complex process and is aected by many
factors.
The truth is, many of the existing protein structures in PDB, except for those simple peptides, are determined
through experimental methods. This can be veried because many of the PDB entries are actually a protein
in complex with other molecules, such as ligands, inhibitors, or is a protein dissolved in a solvent, not the pure
protein alone.
4 Personal Contribution to the Project
My responsibilities in this group project is to realise the storyboard designed by Jialiu Xu by assembling the
video clips, animations, voiceovers together into the nal video.
4.1 My Workow for Contributing to the Video Essay
After receiving the storyboard from Jialiu Xu, I started creating the animation clips that were implementable
using Python with the Manim library. The more complex animations, such as the sickle cell anaemia animations,
were looked up online and directly used in our video with proper in-video citation. Those videos were not created
because the complexity is beyond the requirement of this course.
With Manim, a total of 26 scenes were created (of which only 25 were used as one of them was no longer
applicable after some modications). Some of the designs in the original storyboard were not adopted due to
technical limitations and time constraints.
As for the protein structure models, I fetched them from PDB into ChimeraX. With the built-in functions of
ChimeraX, I colour-coded the structures (mainly by chain) and exported them as
.glb
3D object les. These
les were then imported into Adobe After Eects for simple animating (mainly rotation and zooming).
The animation clips, B-roll footages, 3D animations, and voiceover recordings were assembled together in
Adobe Premiere Pro. Some simple video eects, such as zooming in/out, panning, and fading transitions were
also applied in Premiere Pro to enhance the visual experience.
4.2 Animations Created with Python
Various animation clips were created using Python with the library Manim. The source codes are attached at
the end of this document. For the sake of academic integrity, it is declared that large language models were
involved in writing the following code les. The use of LLMs was mainly for handling complex mathematical
expressions to save up time for actually producing the animations.
4.3 Leadership Role in the Group
Initially, two members were assigned the role as video production. This is impractical as the video editing
software cannot be used collaboratively and only one person can work on the project les at a time. Uploading
the project les to a cloud storage for sharing was also not an option as the les can get very large (several
gigabytes) and the upload/download time would be too long.
Therefore, for easier task delegation, I took the initiative to oer the other video production member to
focus on creating the storyboard from the script. This is eective since I, as a Computer Science student, nd
2
Page 2 of 30
it dicult to come up with creative visual designs from scratch on top of the script. However, with my previous
experience in video editing, I can eectively realise the storyboard into the nal video. Therefore, we agreed on
this division of labour, which greatly improved our productivity and was a successful collaboration.
5 Reection on Learning
5.1 Understanding of Genetics
As I was previously enrolled as an MBBS student, I already have some foundational knowledge of genetics
through trainings from the IASM block. This has equipped me with the necessary background and skills to
understand the complex concepts involved in somatic gene therapy. On the science side, through this project, I
have additional knowledge about the specic applications of somatic gene therapy, such as Luxturna for LCA,
Nusinersen for SMA, etc. On the moral side, I have also learned about more ethical considerations from more
aspects, such as public opinion and fair access to treatment.
5.2 Skills Acquired
By working on this project, I have deepened my skills in professional video production. I have also learned new
skills in 3D molecular visualisation and animation using ChimeraX and Adobe After Eects. Further, in 2D
animation creation, I have improved my skills in using Python with the Manim library to create mathematical
and scientic animations programmatically.
Annex: Python Source Codes for Creating Animations
intro
scenes.py
This le contains code for creating animations used in the introduction section of the video.
1
from manim import *
2
3
# INTRODUCTION SCENES
4
5
class Scene1_TitleText(Scene):
6
"""Opening shot: Somatic Gene Therapy"""
7
def construct(self):
8
# Text animation
9
text = Tex("Science Fiction", font_size=48, color=GREEN)
10
self.play(Write(text))
11
self.wait(2)
12
13
newText = Tex("Somatic Gene Therapy", font_size=48, color=RED)
14
self.play(Transform(text, newText))
15
self.wait(3)
16
17
self.play(FadeOut(text))
18
19
class Scene2_FixingGeneErrorsInACell(Scene):
20
"""Scene: Fixing Gene Errors in a Cell"""
21
def construct(self):
22
# Create cell (outer circle) with background
23
cell = Circle(radius=2.5, color=BLUE, stroke_width=3, fill_color=BLUE, fill_opacity=0.3)
24
25
# Create nucleus (inner circle) - smaller size with background
26
nucleus = Circle(radius=0.9, color=PURPLE, stroke_width=3, fill_color=PURPLE,
fill_opacity=0.35)
,
!
27
28
# Create problematic DNA (red double helix)
29
# Simple representation using two intertwined curves
30
dna_strand1 = ParametricFunction(
31
lambda t: np.array([
3
Page 3 of 30
32
0.3 * np.cos(2 * PI * t),
33
0.8 * t - 0.4,
34
0
35
]),
36
t_range=[0, 1],
37
color=RED
38
)
39
dna_strand2 = ParametricFunction(
40
lambda t: np.array([
41
-0.3 * np.cos(2 * PI * t),
42
0.8 * t - 0.4,
43
0
44
]),
45
t_range=[0, 1],
46
color=RED
47
)
48
problematic_dna = VGroup(dna_strand1, dna_strand2)
49
50
# Create text labels
51
cell_label = Tex("$\\textbf{Cell}$", font_size=28, color=BLUE).next_to(cell, DOWN, buff=0.3)
52
problematic_dna_label = Tex("\\textbf{Problematic \\\\DNA}", font_size=24,
color=RED).next_to(problematic_dna, RIGHT, buff=0.7)
,
!
53
54
# Display cell, nucleus, problematic DNA, and labels at the start
55
self.add(cell, nucleus, problematic_dna, cell_label, problematic_dna_label)
56
self.wait(2)
57
58
# Create fixed DNA (green double helix)
59
fixed_strand1 = ParametricFunction(
60
lambda t: np.array([
61
0.3 * np.cos(2 * PI * t),
62
0.8 * t - 0.4,
63
0
64
]),
65
t_range=[0, 1],
66
color=GREEN
67
)
68
fixed_strand2 = ParametricFunction(
69
lambda t: np.array([
70
-0.3 * np.cos(2 * PI * t),
71
0.8 * t - 0.4,
72
0
73
]),
74
t_range=[0, 1],
75
color=GREEN
76
)
77
fixed_dna = VGroup(fixed_strand1, fixed_strand2)
78
79
# Create fixed DNA label
80
fixed_dna_label = Tex("\\textbf{Fixed \\\\DNA}", font_size=24, color=GREEN).next_to(fixed_dna,
RIGHT, buff=1.0)
,
!
81
82
# Flash effect
83
flash = Flash(problematic_dna.get_center(), color=YELLOW, flash_radius=0.8)
84
85
# Morph DNA to green with pop effect and morph the label
86
self.play(
87
Transform(problematic_dna, fixed_dna),
88
Transform(problematic_dna_label, fixed_dna_label),
89
flash,
90
problematic_dna.animate.scale(1.3).set_color(GREEN)
91
)
92
self.play(problematic_dna.animate.scale(1/1.3))
93
self.wait(2)
4
Page 4 of 30
94
95
class Scene3_NoPassing(Scene):
96
"""Scene: No Passing"""
97
def construct(self):
98
# Start with the ending status of Scene 2
99
cell = Circle(radius=2.5, color=BLUE, stroke_width=3, fill_color=BLUE, fill_opacity=0.3)
100
nucleus = Circle(radius=0.9, color=PURPLE, stroke_width=3, fill_color=PURPLE,
fill_opacity=0.35)
,
!
101
102
# Fixed DNA (green double helix)
103
dna_strand1 = ParametricFunction(
104
lambda t: np.array([
105
0.3 * np.cos(2 * PI * t),
106
0.8 * t - 0.4,
107
0
108
]),
109
t_range=[0, 1],
110
color=GREEN
111
)
112
dna_strand2 = ParametricFunction(
113
lambda t: np.array([
114
-0.3 * np.cos(2 * PI * t),
115
0.8 * t - 0.4,
116
0
117
]),
118
t_range=[0, 1],
119
color=GREEN
120
)
121
fixed_dna = VGroup(dna_strand1, dna_strand2)
122
123
# Create labels
124
cell_label = Tex("$\\textbf{Cell}$", font_size=28, color=BLUE).next_to(cell, DOWN, buff=0.3)
125
fixed_dna_label = Tex("\\textbf{Fixed \\\\DNA}", font_size=24, color=GREEN).next_to(fixed_dna,
RIGHT, buff=1.0)
,
!
126
127
# Group the cell components
128
cell_group = VGroup(cell, nucleus, fixed_dna)
129
130
# Add everything at the start
131
self.add(cell_group, cell_label, fixed_dna_label)
132
133
# Fade out the text labels
134
self.play(FadeOut(cell_label), FadeOut(fixed_dna_label), run_time=0.25)
135
136
# Create stick figures
137
# Parent (taller, on the left)
138
parent_head = Circle(radius=0.3, color=WHITE, stroke_width=2)
139
parent_body = Line(start=ORIGIN, end=DOWN * 1.5, color=WHITE, stroke_width=2)
140
parent_arms = Line(start=LEFT * 0.5, end=RIGHT * 0.5, color=WHITE, stroke_width=2)
141
parent_legs = VGroup(
142
Line(start=ORIGIN, end=DOWN * 0.8 + LEFT * 0.4, color=WHITE, stroke_width=2),
143
Line(start=ORIGIN, end=DOWN * 0.8 + RIGHT * 0.4, color=WHITE, stroke_width=2)
144
)
145
146
parent = VGroup(parent_head, parent_body, parent_arms, parent_legs)
147
parent_head.next_to(parent_body.get_start(), UP, buff=0.1)
148
parent_arms.next_to(parent_body.get_start(), DOWN, buff=0.3)
149
parent_legs.next_to(parent_body.get_end(), DOWN, buff=0)
150
151
parent.move_to(LEFT * 3 + DOWN * 0.5)
152
parent_label = Tex("\\textbf{Parent}", font_size=24, color=WHITE).next_to(parent, DOWN,
buff=0.3)
,
!
153
154
# Child (shorter, on the right)
5
Page 5 of 30
155
child_head = Circle(radius=0.25, color=WHITE, stroke_width=2)
156
child_body = Line(start=ORIGIN, end=DOWN * 1.0, color=WHITE, stroke_width=2)
157
child_arms = Line(start=LEFT * 0.4, end=RIGHT * 0.4, color=WHITE, stroke_width=2)
158
child_legs = VGroup(
159
Line(start=ORIGIN, end=DOWN * 0.6 + LEFT * 0.3, color=WHITE, stroke_width=2),
160
Line(start=ORIGIN, end=DOWN * 0.6 + RIGHT * 0.3, color=WHITE, stroke_width=2)
161
)
162
163
child = VGroup(child_head, child_body, child_arms, child_legs)
164
child_head.next_to(child_body.get_start(), UP, buff=0.1)
165
child_arms.next_to(child_body.get_start(), DOWN, buff=0.2)
166
child_legs.next_to(child_body.get_end(), DOWN, buff=0)
167
168
child.move_to(RIGHT * 3 + DOWN * 0.3)
169
child_label = Tex("\\textbf{Child}", font_size=24, color=WHITE).next_to(child, DOWN, buff=0.3)
170
171
# Fade in stick figures and their labels
172
self.play(
173
FadeIn(parent), FadeIn(parent_label),
174
FadeIn(child), FadeIn(child_label),
175
cell_group.animate.scale(0.3).shift(parent.get_center() + RIGHT * 1.2),
176
run_time=1
177
)
178
179
# Move cell next to parent
180
self.play(cell_group.animate.move_to(parent.get_center() + RIGHT * 1.2), run_time=0.5)
181
self.wait(0.25)
182
183
# Draw arrow from left to right
184
arrow = Arrow(
185
start=LEFT * 1.5,
186
end=RIGHT * 1.5,
187
color=YELLOW,
188
buff=0,
189
stroke_width=6
190
).move_to(DOWN * 0.5)
191
self.play(Create(arrow), run_time=0.25)
192
193
# Cell attempts to move along arrow but is stopped by red cross
194
# Create red cross in the middle
195
cross_line1 = Line(start=UP * 0.3 + LEFT * 0.3, end=DOWN * 0.3 + RIGHT * 0.3, color=RED,
stroke_width=8)
,
!
196
cross_line2 = Line(start=UP * 0.3 + RIGHT * 0.3, end=DOWN * 0.3 + LEFT * 0.3, color=RED,
stroke_width=8)
,
!
197
red_cross = VGroup(cross_line1, cross_line2).move_to(DOWN * 0.5)
198
199
# Animate cell moving and being stopped
200
self.play(
201
cell_group.animate.move_to(cell_group.get_center() + RIGHT * 1.5),
202
run_time=1,
203
rate_func=rush_into
204
)
205
206
# Show red cross appearing and cell bouncing back slightly
207
self.play(Create(red_cross), cell_group.animate.shift(LEFT * 0.3), run_time=0.5)
208
self.wait(2)
application eyes.py
This le contains code for creating animations about gene therapy applications for eye diseases, specically
Luxturna treatment for Leber's Congenital Amaurosis (LCA).
6
Page 6 of 30
1
from manim import *
2
3
# APPLICATION - EYES SCENES
4
5
class Scene4_Chapter1Title(Scene):
6
"""Chapter Title: Application - Eyes"""
7
def construct(self):
8
# Text animation
9
chapter = Tex("{\\scshape\\bfseries CHAPTER I}", font_size=50, color=YELLOW)
10
title = Tex("{\\bfseries Genetic Blindness}", font_size=64, color=YELLOW)
11
separator = Line(start=LEFT * 3, end=RIGHT * 3, color=ORANGE, stroke_width=4)
12
13
chapter.move_to(UP * 0.75)
14
title.move_to(DOWN * 0.75)
15
separator.move_to(ORIGIN)
16
17
self.play(
18
Write(chapter, run_time=1.5),
19
Create(separator, run_time=1.5),
20
Write(title, run_time=1.5)
21
)
22
23
self.wait(3)
24
25
class Scene5_LuxturnaAndLCATitle(Scene):
26
"""Title: Luxturna and LCA"""
27
def construct(self):
28
# Text animation
29
title = Tex("{\\bfseries Luxturna}", font_size=64, color=BLUE)
30
subtitle = Tex("A gene therapy for", font_size=36)
31
disease = Tex("{\\bfseries Leber Congenital Amaurosis (LCA)}", font_size=40, color=RED)
32
33
title.move_to(UP * 1)
34
subtitle.move_to(DOWN * 0.2)
35
disease.move_to(DOWN * 0.8)
36
37
self.play(Write(title, run_time=0.75))
38
self.wait(3)
39
self.play(Write(subtitle), Write(disease), run_time=0.75)
40
41
self.wait(3)
42
43
class Scene6_LuxturnaPacking(Scene):
44
"""Luxturna Packing Animation"""
45
def construct(self):
46
scene_title = Tex("{\\bfseries Luxturna Mechanism}", font_size=48, color=YELLOW)
47
scene_title.move_to(UP * 3)
48
self.play(Write(scene_title), run_time=1)
49
self.wait(0.5)
50
51
# 1. Create cDNA (green single strand) on the left
52
cdna = ParametricFunction(
53
lambda t: np.array([
54
0.2 * np.sin(4 * PI * t),
55
2 * t - 1,
56
0
57
]),
58
t_range=[0, 1],
59
color=GREEN,
60
stroke_width=6
61
)
62
7
Page 7 of 30
63
cdna_label1 = Tex("\\textbf{cDNA}", font_size=28, color=GREEN)
64
cdna_label2 = Tex("\\textbf{(functional RPE65)}", font_size=24, color=GREEN)
65
cdna_labels = VGroup(cdna_label1, cdna_label2).arrange(DOWN, buff=0.2)
66
67
cdna.move_to(LEFT * 4)
68
cdna_labels.next_to(cdna, DOWN, buff=0.5)
69
70
# 2. Create AAV viral vector (purple capsid) on the right
71
# Represent as a hexagonal/circular capsid with inner space
72
aav_capsid = RegularPolygon(n=6, radius=1.2, color=PURPLE, stroke_width=4, fill_color=PURPLE,
fill_opacity=0.2)
,
!
73
74
# Add spike proteins around the capsid
75
spike_positions = [
76
UP * 1.2,
77
UP * 0.6 + RIGHT * 1.0,
78
DOWN * 0.6 + RIGHT * 1.0,
79
DOWN * 1.2,
80
DOWN * 0.6 + LEFT * 1.0,
81
UP * 0.6 + LEFT * 1.0
82
]
83
84
spikes = VGroup()
85
for pos in spike_positions:
86
spike = Triangle(color=PURPLE, fill_color=PURPLE, fill_opacity=0.8)
87
spike.scale(0.15)
88
spike.move_to(pos)
89
# Point spike outward from center
90
angle = np.arctan2(pos[1], pos[0])
91
spike.rotate(angle + PI/2)
92
spikes.add(spike)
93
94
aav_vector = VGroup(aav_capsid, spikes)
95
96
aav_label = Tex("\\textbf{AAV therapeutic\\\\vector}", font_size=28, color=PURPLE)
97
98
aav_vector.move_to(RIGHT * 4)
99
aav_label.next_to(aav_vector, DOWN, buff=0.5)
100
101
# Display both components
102
self.play(
103
Create(cdna),
104
Write(cdna_labels),
105
run_time=0.7
106
)
107
self.wait(1.5)
108
self.play(
109
Create(aav_vector),
110
Write(aav_label),
111
run_time=0.7
112
)
113
self.wait(2)
114
115
# 3. Move cDNA into the viral vector
116
# Scale down cDNA to fit inside
117
self.play(
118
cdna.animate.scale(0.4).move_to(aav_vector.get_center()),
119
FadeOut(cdna_labels),
120
run_time=1
121
)
122
self.wait(0.5)
123
124
# Group the combination
125
aav_with_cdna = VGroup(aav_vector, cdna)
8
Page 8 of 30
126
127
# 4. Zoom and move to center, transform label
128
aav_new_label = Tex("\\textbf{AAV2 serotype}", font_size=32, color=PURPLE)
129
aav_new_label.move_to(DOWN * 2.5)
130
131
self.play(
132
aav_with_cdna.animate.scale(1.5).move_to(ORIGIN),
133
Transform(aav_label, aav_new_label),
134
run_time=1
135
)
136
self.wait(3)
137
138
class Scene7_LuxturnaInjection(Scene):
139
"""Luxturna Injection Animation"""
140
def construct(self):
141
scene_title = Tex("{\\bfseries Luxturna Mechanism}", font_size=48, color=YELLOW)
142
scene_title.move_to(UP * 3)
143
self.add(scene_title)
144
145
# 1. Start from where Scene 6 ended - recreate the AAV2 with cDNA at center
146
aav_capsid = RegularPolygon(n=6, radius=1.2, color=PURPLE, stroke_width=4, fill_color=PURPLE,
fill_opacity=0.2)
,
!
147
148
spike_positions = [
149
UP * 1.2,
150
UP * 0.6 + RIGHT * 1.0,
151
DOWN * 0.6 + RIGHT * 1.0,
152
DOWN * 1.2,
153
DOWN * 0.6 + LEFT * 1.0,
154
UP * 0.6 + LEFT * 1.0
155
]
156
157
spikes = VGroup()
158
for pos in spike_positions:
159
spike = Triangle(color=PURPLE, fill_color=PURPLE, fill_opacity=0.8)
160
spike.scale(0.15)
161
spike.move_to(pos)
162
angle = np.arctan2(pos[1], pos[0])
163
spike.rotate(angle + PI/2)
164
spikes.add(spike)
165
166
aav_vector = VGroup(aav_capsid, spikes)
167
168
cdna = ParametricFunction(
169
lambda t: np.array([
170
0.2 * np.sin(4 * PI * t),
171
2 * t - 1,
172
0
173
]),
174
t_range=[0, 1],
175
color=GREEN,
176
stroke_width=6
177
).scale(0.4)
178
179
aav_with_cdna = VGroup(aav_vector, cdna).scale(1.5).move_to(ORIGIN)
180
aav_label = Tex("\\textbf{AAV2 serotype}", font_size=32, color=PURPLE).move_to(DOWN * 2.5)
181
182
self.add(aav_with_cdna, aav_label)
183
184
# 2. Zoom out AAV2 and move to left, create impaired cell on right-center
185
self.play(
186
aav_with_cdna.animate.scale(0.5).move_to(LEFT * 4),
187
FadeOut(aav_label),
188
run_time=1
9
Page 9 of 30
189
)
190
191
# Create cell with impaired DNA (red) in nucleus
192
cell = Circle(radius=2, color=BLUE, stroke_width=3, fill_color=BLUE, fill_opacity=0.1)
193
nucleus = Circle(radius=0.8, color=PURPLE, stroke_width=3, fill_color=PURPLE,
fill_opacity=0.15)
,
!
194
195
# Impaired DNA (red)
196
impaired_dna = ParametricFunction(
197
lambda t: np.array([
198
0.2 * np.sin(4 * PI * t),
199
0.6 * t - 0.3,
200
0
201
]),
202
t_range=[0, 1],
203
color=RED,
204
stroke_width=4
205
)
206
207
cell_group = VGroup(cell, nucleus, impaired_dna)
208
cell_group.move_to(RIGHT * 1.5)
209
210
# Add cell label for impaired state
211
cell_label = Tex("\\textbf{Cell (impaired DNA)}", font_size=32, color=RED)
212
cell_label.next_to(cell_group, DOWN, buff=0.3)
213
214
self.play(Create(cell_group), Write(cell_label), run_time=1)
215
216
# 3. Vector moves towards cell and releases cDNA
217
self.play(
218
aav_with_cdna.animate.move_to(cell.get_left() + LEFT * 0.5),
219
run_time=1.2
220
)
221
222
# Extract and scale up the cDNA for delivery
223
cdna_delivery = cdna.copy().scale(2)
224
225
# Create fixed cell label
226
fixed_cell_label = Tex("\\textbf{Cell (fixed DNA)}", font_size=32, color=GREEN)
227
fixed_cell_label.next_to(cell_group, DOWN, buff=0.3)
228
229
self.play(
230
cdna_delivery.animate.move_to(nucleus.get_center()),
231
impaired_dna.animate.set_color(GREEN),
232
Transform(cell_label, fixed_cell_label),
233
run_time=1.5
234
)
235
236
# Remove the delivery cDNA and keep the transformed one
237
self.remove(cdna_delivery)
238
239
# 4. Vector fades out, cell moves to center and zooms slightly
240
self.play(FadeOut(aav_with_cdna), run_time=0.5)
241
242
self.play(
243
cell_group.animate.scale(0.9).move_to(ORIGIN),
244
cell_label.animate.next_to(ORIGIN + DOWN * 2, DOWN, buff=0),
245
run_time=1
246
)
247
248
# 5. Cell produces functional retinoid isomerase (blue hexagons)
249
enzyme_label = Tex("\\textbf{Functional Retinoid\\\\Isomerase (RPE65)}", font_size=32,
color=BLUE)
,
!
250
enzyme_label.move_to(DOWN * 3)
10
Page 10 of 30
251
252
# Create enzymes with fixed random positions
253
enzyme_positions = [
254
UP * 2 + LEFT * 5,
255
UP * 1.5 + RIGHT * 5.5,
256
UP * 0.5 + LEFT * 6,
257
DOWN * 0.8 + RIGHT * 6,
258
DOWN * 2 + LEFT * 5.5,
259
DOWN * 2.5 + RIGHT * 4.5,
260
UP * 2.8 + LEFT * 2,
261
UP * 2.5 + RIGHT * 3,
262
DOWN * 3 + LEFT * 3,
263
DOWN * 2.8 + RIGHT * 2.5,
264
UP * 1 + LEFT * 3.5,
265
DOWN * 1.5 + LEFT * 4
266
]
267
268
enzymes = VGroup()
269
animations = []
270
271
for i, pos in enumerate(enzyme_positions):
272
enzyme = RegularPolygon(n=6, radius=0.15, color=BLUE, fill_color=BLUE, fill_opacity=0.7)
273
enzyme.move_to(cell.get_center())
274
enzymes.add(enzyme)
275
276
# Stagger the animations slightly
277
animations.append(
278
AnimationGroup(
279
enzyme.animate.move_to(pos),
280
lag_ratio=0.1
281
)
282
)
283
284
self.add(enzymes)
285
286
# Animate enzymes leaving the cell
287
self.play(
288
LaggedStart(*[enzyme.animate.move_to(pos) for enzyme, pos in zip(enzymes,
enzyme_positions)],
,
!
289
lag_ratio=0.08),
290
Write(enzyme_label),
291
run_time=2.8
292
)
293
294
self.wait(2)
295
296
class Scene8_ClinicalResultsEyes(Scene):
297
"""Clinical Results Text"""
298
def construct(self):
299
# Title
300
title = Tex("{\\bfseries Clinical Results}", font_size=56, color=YELLOW)
301
title.move_to(UP * 2.5)
302
303
# Result statements
304
result1 = Tex("$\\bullet$ Significant improvements in retinal function", font_size=32)
305
result2 = Tex("$\\bullet$ Increased light sensitivity", font_size=32)
306
result3 = Tex("$\\bullet$ Enhanced pupillary responses", font_size=32)
307
result4 = Tex("$\\bullet$ Improved vision in dim environments", font_size=32, color=GREEN)
308
309
results = VGroup(result1, result2, result3, result4).arrange(DOWN, buff=0.5,
aligned_edge=LEFT)
,
!
310
results.move_to(DOWN * 0.5)
311
312
# Animate title
11
Page 11 of 30
313
self.play(Write(title), run_time=1)
314
self.wait(0.5)
315
316
# Animate results appearing one by one
317
self.play(FadeIn(result1, shift=UP * 0.3), run_time=0.8)
318
self.wait(0.3)
319
self.play(FadeIn(result2, shift=UP * 0.3), run_time=0.8)
320
self.wait(0.3)
321
self.play(FadeIn(result3, shift=UP * 0.3), run_time=0.8)
322
self.wait(0.3)
323
self.play(FadeIn(result4, shift=UP * 0.3), run_time=0.8)
324
325
self.wait(3)
application blood disorder.py
This le contains code for creating animations about gene therapy applications for blood disorders, specically
CRISPR treatment for sickle cell disease.
1
from manim import *
2
3
# BLOOD DISORDER APPLICATION SCENES
4
5
class Scene9_Chapter2Title(Scene):
6
"""Chapter 2 Title: Gene Therapy for Blood Disorders"""
7
def construct(self):
8
# Text animation
9
chapter = Tex("{\\scshape\\bfseries CHAPTER II}", font_size=50, color=YELLOW)
10
title = Tex("{\\bfseries Blood Disorders}", font_size=64, color=YELLOW)
11
separator = Line(start=LEFT * 3, end=RIGHT * 3, color=ORANGE, stroke_width=4)
12
13
chapter.move_to(UP * 0.75)
14
title.move_to(DOWN * 0.75)
15
separator.move_to(ORIGIN)
16
17
self.play(
18
Write(chapter, run_time=1.5),
19
Create(separator, run_time=1.5),
20
Write(title, run_time=1.5)
21
)
22
23
self.wait(3)
24
25
class Scene10_SickleCellDiseaseTitle(Scene):
26
"""Sickle Cell Disease Title Scene"""
27
def construct(self):
28
# Text animation
29
title = Tex("{\\bfseries Sickle Cell Disease}", font_size=72, color=YELLOW)
30
31
self.play(Write(title, run_time=1))
32
33
self.wait(3)
34
35
class Scene11_CRISPRTreatment(Scene):
36
"""CRISPR-Cas9 Treatment for Sickle Cell Disease"""
37
def construct(self):
38
# Part 1: Show BCL11A gene suppressing fetal hemoglobin
39
bcl11a_gene = Rectangle(width=2, height=0.8, color=RED, fill_color=RED, fill_opacity=0.3)
40
bcl11a_label = Tex("\\textbf{BCL11A\\\\gene}", font_size=24, color=RED)
41
bcl11a_label.next_to(bcl11a_gene, UP, buff=0.3)
42
43
bcl11a_group = VGroup(bcl11a_gene, bcl11a_label)
12
Page 12 of 30
44
bcl11a_group.move_to(UP * 2 + LEFT * 3)
45
46
# Fetal hemoglobin (suppressed, shown as small gray circles)
47
fetal_hb_suppressed = VGroup(*[
48
Circle(radius=0.15, color=GRAY, fill_color=GRAY, fill_opacity=0.4)
49
for _ in range(3)
50
]).arrange(RIGHT, buff=0.3)
51
fetal_hb_suppressed.move_to(DOWN * 1 + LEFT * 3)
52
53
fetal_label = Tex("\\textbf{Fetal Hb\\\\(suppressed)}", font_size=20, color=GRAY)
54
fetal_label.next_to(fetal_hb_suppressed, DOWN, buff=0.3)
55
56
# Suppression arrow
57
suppression_arrow = Arrow(
58
start=bcl11a_gene.get_bottom(),
59
end=fetal_hb_suppressed.get_top(),
60
color=RED,
61
stroke_width=6
62
)
63
64
self.play(
65
Create(bcl11a_group),
66
Create(suppression_arrow),
67
Create(fetal_hb_suppressed),
68
Write(fetal_label),
69
run_time=1.5
70
)
71
self.wait(1)
72
73
# Part 2: Show CRISPR-Cas9 coming in to edit BCL11A
74
crispr_cas9 = VGroup(
75
Rectangle(width=1.5, height=0.6, color=BLUE, fill_color=BLUE, fill_opacity=0.5),
76
Tex("\\textbf{CRISPR-\\\\Cas9}", font_size=20, color=BLUE)
77
)
78
crispr_cas9[1].move_to(crispr_cas9[0].get_center())
79
crispr_cas9.move_to(UP * 2 + RIGHT * 2)
80
81
self.play(Create(crispr_cas9), run_time=1)
82
self.wait(0.5)
83
84
# CRISPR moves to BCL11A
85
self.play(crispr_cas9.animate.move_to(bcl11a_gene.get_center()), run_time=1.5)
86
87
# Flash effect showing gene editing
88
flash = Flash(bcl11a_gene.get_center(), color=YELLOW, flash_radius=1)
89
self.play(flash)
90
91
# BCL11A becomes deactivated (crossed out)
92
cross_line1 = Line(
93
start=bcl11a_gene.get_corner(UL),
94
end=bcl11a_gene.get_corner(DR),
95
color=YELLOW,
96
stroke_width=6
97
)
98
cross_line2 = Line(
99
start=bcl11a_gene.get_corner(UR),
100
end=bcl11a_gene.get_corner(DL),
101
color=YELLOW,
102
stroke_width=6
103
)
104
105
deactivated_label = Tex("\\textbf{BCL11A\\\\(deactivated)}", font_size=24, color=GRAY)
106
deactivated_label.move_to(bcl11a_label.get_center())
13
Page 13 of 30
107
108
self.play(
109
Create(cross_line1),
110
Create(cross_line2),
111
Transform(bcl11a_label, deactivated_label),
112
FadeOut(crispr_cas9),
113
suppression_arrow.animate.set_color(GRAY).set_opacity(0.3),
114
run_time=1.5
115
)
116
self.wait(1)
117
118
# Part 3: Fetal hemoglobin production resumes
119
fetal_hb_active = VGroup(*[
120
Circle(radius=0.2, color=GREEN, fill_color=GREEN, fill_opacity=0.7)
121
for _ in range(6)
122
]).arrange_in_grid(rows=2, cols=3, buff=0.3)
123
fetal_hb_active.move_to(fetal_hb_suppressed.get_center() + DOWN * 0.5)
124
125
active_label = Tex("\\textbf{Fetal Hb\\\\(high-level)}", font_size=20, color=GREEN)
126
active_label.next_to(fetal_hb_active, DOWN, buff=0.3)
127
128
self.play(
129
Transform(fetal_hb_suppressed, fetal_hb_active),
130
Transform(fetal_label, active_label),
131
run_time=1.5
132
)
133
self.wait(1)
134
135
# Part 4: Show effect on red blood cells
136
# Fade everything out
137
self.play(
138
FadeOut(bcl11a_group),
139
FadeOut(cross_line1),
140
FadeOut(cross_line2),
141
FadeOut(suppression_arrow),
142
FadeOut(fetal_hb_suppressed),
143
FadeOut(fetal_label),
144
run_time=1
145
)
146
147
# 1. Create sickle cells and normal hemoglobin scattered across screen
148
# Sickle cells (red crescents)
149
sickle_positions = [
150
UP * 2.5 + LEFT * 4,
151
UP * 1.5 + LEFT * 1,
152
UP * 0.5 + LEFT * 5,
153
DOWN * 0.5 + LEFT * 2.5,
154
DOWN * 1.5 + LEFT * 5.5,
155
UP * 2 + RIGHT * 1,
156
DOWN * 2 + LEFT * 0.5,
157
]
158
159
sickle_cells = VGroup()
160
for pos in sickle_positions:
161
arc1 = Arc(radius=0.3, angle=PI, color=RED, stroke_width=3, fill_color=RED,
fill_opacity=0.4)
,
!
162
arc2 = Arc(radius=0.25, angle=-PI, color=RED, stroke_width=3, fill_color=RED,
fill_opacity=0.4).next_to(arc1, RIGHT, buff=0)
,
!
163
sickle = VGroup(arc1, arc2).rotate(PI/4)
164
sickle.move_to(pos)
165
sickle_cells.add(sickle)
166
167
# Normal hemoglobin (green circles)
168
normal_hb_positions = [
14
Page 14 of 30
169
UP * 3 + LEFT * 2,
170
UP * 1 + RIGHT * 4,
171
DOWN * 1 + RIGHT * 5,
172
DOWN * 2.5 + RIGHT * 2,
173
UP * 0.5 + RIGHT * 2,
174
]
175
176
normal_hbs = VGroup()
177
for pos in normal_hb_positions:
178
normal_hb = Circle(radius=0.25, color=GREEN, fill_color=GREEN, fill_opacity=0.5,
stroke_width=3)
,
!
179
normal_hb.move_to(pos)
180
normal_hbs.add(normal_hb)
181
182
# Legend at bottom left
183
legend_box = Rectangle(width=3.5, height=1.8, color=WHITE, stroke_width=2)
184
legend_box.move_to(DOWN * 2.7 + LEFT * 4.5)
185
186
# Legend items
187
sickle_legend_icon = VGroup(
188
Arc(radius=0.15, angle=PI, color=RED, stroke_width=2, fill_color=RED, fill_opacity=0.4),
189
)
190
sickle_legend_icon[0].next_to(sickle_legend_icon[0], RIGHT, buff=0)
191
sickle_legend_label = Tex("Sickle Hb", font_size=18, color=RED)
192
sickle_legend = VGroup(sickle_legend_icon, sickle_legend_label).arrange(RIGHT, buff=0.3)
193
194
normal_legend_icon = Circle(radius=0.15, color=GREEN, fill_color=GREEN, fill_opacity=0.5,
stroke_width=2)
,
!
195
normal_legend_label = Tex("Normal Hb", font_size=18, color=GREEN)
196
normal_legend = VGroup(normal_legend_icon, normal_legend_label).arrange(RIGHT, buff=0.3)
197
198
fetal_legend_icon = Circle(radius=0.15, color=BLUE, fill_color=BLUE, fill_opacity=0.5,
stroke_width=2)
,
!
199
fetal_legend_label = Tex("Fetal Hb", font_size=18, color=BLUE)
200
fetal_legend = VGroup(fetal_legend_icon, fetal_legend_label).arrange(RIGHT, buff=0.3)
201
202
legend_items = VGroup(sickle_legend, normal_legend, fetal_legend).arrange(DOWN,
aligned_edge=LEFT, buff=0.2)
,
!
203
legend_items.move_to(legend_box.get_center())
204
205
legend_group = VGroup(legend_box, legend_items)
206
207
# 2. Counter at bottom right showing functional hemoglobin percentage
208
counter_box = Rectangle(width=3, height=1.2, color=WHITE, stroke_width=2)
209
counter_box.move_to(DOWN * 2.9 + RIGHT * 4.5)
210
211
counter_label = Tex("\\textbf{Functional Hb}", font_size=20)
212
counter_label.move_to(counter_box.get_center() + UP * 0.3)
213
214
initial_percentage = int((len(normal_hbs) / (len(sickle_cells) + len(normal_hbs))) * 100)
215
counter_value = Tex(f"\\textbf{{{initial_percentage}\\%}}", font_size=32, color=YELLOW)
216
counter_value.move_to(counter_box.get_center() + DOWN * 0.25)
217
218
counter_group = VGroup(counter_box, counter_label, counter_value)
219
220
# Fade in everything
221
self.play(
222
Create(sickle_cells),
223
Create(normal_hbs),
224
Create(legend_group),
225
Create(counter_group),
226
run_time=1.5
227
)
228
self.wait(1)
15
Page 15 of 30
229
230
# 3. Fade in fetal hemoglobin (blue circles) and update counter
231
fetal_hb_positions = [
232
UP * 2.8 + RIGHT * 3.5,
233
UP * 0.8 + LEFT * 3.5,
234
UP * 1.8 + RIGHT * 5.5,
235
DOWN * 0.3 + RIGHT * 0.5,
236
DOWN * 1.8 + RIGHT * 4.5,
237
DOWN * 2.5 + LEFT * 3,
238
UP * 3.2 + LEFT * 0.5,
239
DOWN * 0.8 + LEFT * 4.5,
240
]
241
242
fetal_hbs = VGroup()
243
for pos in fetal_hb_positions:
244
fetal_hb = Circle(radius=0.25, color=BLUE, fill_color=BLUE, fill_opacity=0.5,
stroke_width=3)
,
!
245
fetal_hb.move_to(pos)
246
fetal_hbs.add(fetal_hb)
247
248
# Calculate new percentage
249
new_percentage = int((len(normal_hbs) + len(fetal_hbs)) / (len(sickle_cells) + len(normal_hbs)
+ len(fetal_hbs)) * 100)
,
!
250
new_counter_value = Tex(f"\\textbf{{{new_percentage}\\%}}", font_size=32, color=GREEN)
251
new_counter_value.move_to(counter_value.get_center())
252
253
self.play(
254
FadeIn(fetal_hbs, lag_ratio=0.1),
255
Transform(counter_value, new_counter_value),
256
run_time=2
257
)
258
self.wait(1.5)
259
260
# Final message
261
cure_text = Tex("\\textbf{Malfunctioned Haemoglobin Diluted}", font_size=40, color=WHITE)
262
cure_text_box = Rectangle(width=8, height=1, color=GREEN, stroke_width=3, fill_color=GREEN,
fill_opacity=0.3)
,
!
263
cure_text.move_to(ORIGIN)
264
265
self.play(Create(cure_text_box), Write(cure_text), run_time=1)
266
self.wait(2)
application blood cancer.py
This le contains code for creating animations about gene therapy applications for blood cancer, specically
CAR-T cell therapy for leukemia and its side eects.
1
from manim import *
2
import random
3
4
# BLOOD CANCER APPLICATION SCENES
5
6
class Scene12_Chapter3Title(Scene):
7
"""Chapter 3 Title: Leukaemia and Lymphoma"""
8
def construct(self):
9
# Text animation
10
chapter = Tex("{\\scshape\\bfseries CHAPTER III}", font_size=50, color=YELLOW)
11
title = Tex("{\\bfseries Leukaemia and Lymphoma}", font_size=64, color=YELLOW)
12
separator = Line(start=LEFT * 3, end=RIGHT * 3, color=ORANGE, stroke_width=4)
13
14
chapter.move_to(UP * 0.75)
15
title.move_to(DOWN * 0.75)
16
Page 16 of 30
16
separator.move_to(ORIGIN)
17
18
self.wait(1)
# for editing
19
20
self.play(
21
Write(chapter, run_time=1.5),
22
Create(separator, run_time=1.5),
23
Write(title, run_time=1.5)
24
)
25
26
self.wait(3)
27
28
class Scene13_WBCDivision(Scene):
29
"""White Blood Cell Division and Mutation Introduction Scene"""
30
def construct(self):
31
# Create initial white blood cell
32
initial_cell = Circle(radius=0.3, color=WHITE, fill_opacity=0.8, fill_color=WHITE,
stroke_width=2)
,
!
33
initial_cell.move_to(ORIGIN)
34
35
# Store all cells in a list
36
cells = [initial_cell]
37
38
self.add(initial_cell)
39
self.wait(1)
40
41
# Division loop
42
max_cells = 100
43
division_interval = 0.15
# Time between divisions
44
cell_radius = 0.3
45
46
def find_non_overlapping_position(parent_pos, existing_cells, max_attempts=50):
47
"""Find a position for new cell that doesnt overlap with existing cells"""
48
for attempt in range(max_attempts):
49
angle = np.random.uniform(0, 2 * np.pi)
50
distance = cell_radius * 2.5
# Start at safe distance
51
offset = np.array([np.cos(angle), np.sin(angle), 0]) * distance
52
new_pos = parent_pos + offset
53
54
# Check if position is valid (not overlapping and within frame)
55
if abs(new_pos[0]) < config.frame_width / 2 - cell_radius and \
56
abs(new_pos[1]) < config.frame_height / 2 - cell_radius:
57
58
# Check overlap with existing cells
59
overlapping = False
60
for cell in existing_cells:
61
dist = np.linalg.norm(new_pos - cell.get_center())
62
if dist < cell_radius * 2.2:
# Minimum safe distance
63
overlapping = True
64
break
65
66
if not overlapping:
67
return new_pos
68
69
# If no good position found, return random position with larger offset
70
angle = np.random.uniform(0, 2 * np.pi)
71
distance = cell_radius * 4
72
offset = np.array([np.cos(angle), np.sin(angle), 0]) * distance
73
return parent_pos + offset
74
75
while len(cells) < max_cells:
76
# Select a random cell to divide from all existing cells
77
if len(cells) > 0:
78
parent = random.choice(cells)
17
Page 17 of 30
79
parent_pos = parent.get_center()
80
81
# Find positions for two daughter cells
82
pos1 = find_non_overlapping_position(parent_pos, cells)
83
84
# Create first daughter cell
85
new_cell1 = Circle(radius=cell_radius, color=WHITE, fill_opacity=0.8,
fill_color=WHITE, stroke_width=2)
,
!
86
new_cell1.move_to(parent_pos)
87
88
# Temporarily add to list to check for second position
89
temp_cells = cells + [new_cell1]
90
pos2 = find_non_overlapping_position(parent_pos, temp_cells)
91
92
# Create second daughter cell
93
new_cell2 = Circle(radius=cell_radius, color=WHITE, fill_opacity=0.8,
fill_color=WHITE, stroke_width=2)
,
!
94
new_cell2.move_to(parent_pos)
95
96
# Remove parent cell and add daughter cells
97
self.remove(parent)
98
cells.remove(parent)
99
100
cells.append(new_cell1)
101
cells.append(new_cell2)
102
103
self.add(new_cell1, new_cell2)
104
105
# Animate cells moving to their positions
106
self.play(
107
new_cell1.animate.move_to(pos1),
108
new_cell2.animate.move_to(pos2),
109
run_time=0.3,
110
rate_func=smooth
111
)
112
113
if len(cells) >= max_cells:
114
break
115
116
self.wait(2)
117
118
class Scene14_CARTCellTherapy(Scene):
119
"""CAR T-cell Therapy Process"""
120
def construct(self):
121
# Text animation
122
title = Tex("{\\bfseries CAR-T Cell Therapy}", font_size=72, color=YELLOW)
123
124
self.wait(2)
# for editing
125
126
self.play(Write(title, run_time=1))
127
128
self.wait(3)
129
130
class Scene15_HighRateBut(Scene):
131
def construct(self):
132
# Text animation
133
text = Tex("\\textbf{High Remission Rate}", font_size=64, color=YELLOW)
134
text.move_to(UP * 0.5)
135
self.wait(1.5)
136
self.play(Write(text, run_time=1))
137
self.wait(1)
138
139
but_text = Tex("\\textbf{But...?}", font_size=64, color=RED)
140
but_text.move_to(DOWN * 0.5)
18
Page 18 of 30
141
self.play(Write(but_text, run_time=1))
142
self.wait(2)
143
144
class Scene16_CytokineStorm(Scene):
145
"""Cytokine Storm Explanation Scene"""
146
def construct(self):
147
# 1. T cell
148
t_cell = Circle(radius=0.5, color=BLUE, fill_color=BLUE, fill_opacity=0.5, stroke_width=3)
149
t_cell.move_to(UP * 2.5)
150
t_cell_label = Tex("\\textbf{T Cell}", font_size=24, color=BLUE).next_to(t_cell, DOWN,
buff=0.3)
,
!
151
t_cell_group = VGroup(t_cell, t_cell_label)
152
153
# 2. Cancer Cell
154
cancer_cell = Circle(radius=0.5, color=RED, fill_color=RED, fill_opacity=0.5, stroke_width=3)
155
cancer_cell.move_to(DOWN * 2.5 + LEFT * 3)
156
cancer_cell_label = Tex("\\textbf{Cancer Cell}", font_size=24, color=RED).next_to(cancer_cell,
DOWN, buff=0.3)
,
!
157
cancer_cell_group = VGroup(cancer_cell, cancer_cell_label)
158
159
# 3. Healthy Cell
160
healthy_cell = Circle(radius=0.5, color=GREEN, fill_color=GREEN, fill_opacity=0.5,
stroke_width=3)
,
!
161
healthy_cell.move_to(DOWN * 2.5 + RIGHT * 3)
162
healthy_cell_label = Tex("\\textbf{Healthy Cell}", font_size=24,
color=GREEN).next_to(healthy_cell, DOWN, buff=0.3)
,
!
163
healthy_cell_group = VGroup(healthy_cell, healthy_cell_label)
164
165
# arrows
166
arrow_to_cancer = Arrow(
167
start=t_cell_group.get_bottom(),
168
end=cancer_cell_group.get_top() + DOWN * 0.1,
169
color=YELLOW,
170
buff=0.5,
171
stroke_width=6
172
)
173
174
arrow_to_healthy = Arrow(
175
start=t_cell_group.get_bottom(),
176
end=healthy_cell_group.get_top() + DOWN * 0.1,
177
color=YELLOW,
178
buff=0.5,
179
stroke_width=6
180
)
181
182
# text
183
text = Tex("\\textbf{Cytokine Storm}", font_size=48, color=ORANGE)
184
text.next_to(arrow_to_healthy.get_center(), RIGHT, buff=1)
185
186
self.wait(1)
187
self.play(
188
Create(t_cell), Write(t_cell_label),
189
Create(cancer_cell), Write(cancer_cell_label),
190
Create(healthy_cell), Write(healthy_cell_label),
191
run_time=0.5
192
)
193
self.wait(1)
194
self.play(Create(arrow_to_cancer), run_time=0.5)
195
self.play(Create(arrow_to_healthy), Write(text), run_time=0.5)
196
197
self.wait(3)
19
Page 19 of 30
application neuromuscular.py
This le contains code for creating animations about gene therapy applications for neuromuscular diseases,
specically Nusinersen therapy for Spinal Muscular Atrophy (SMA).
1
from manim import *
2
3
# NEUROMUSCULAR DISEASE APPLICATION SCENES
4
5
class Scene17_Chapter4Title(Scene):
6
def construct(self):
7
# Text animation
8
chapter = Tex("{\\scshape\\bfseries CHAPTER IV}", font_size=50, color=YELLOW)
9
title = Tex("{\\bfseries Spinal Muscular Atrophy}", font_size=64, color=YELLOW)
10
separator = Line(start=LEFT * 3, end=RIGHT * 3, color=ORANGE, stroke_width=4)
11
12
chapter.move_to(UP * 0.75)
13
title.move_to(DOWN * 0.75)
14
separator.move_to(ORIGIN)
15
16
self.play(
17
Write(chapter, run_time=1.5),
18
Create(separator, run_time=1.5),
19
Write(title, run_time=1.5)
20
)
21
22
self.wait(3)
23
24
class Scene18_BackupSMN2Gene(Scene):
25
def construct(self):
26
# title
27
title = Tex("\\textbf{SMN2 Gene As a Backup}", font_size=48, color=YELLOW)
28
title.move_to(UP * 3)
29
self.play(Write(title), run_time=1)
30
self.wait(1)
31
32
# A segment of SMN2 RNA, represented by two parallel wavy lines (sine waves)
33
x_start = -6
34
x_end = 6
35
amplitude = 0.3
36
frequency = 1
37
wave_func = lambda x: amplitude * np.sin(frequency * x)
38
smn2_rna = VGroup(
39
ParametricFunction(
40
lambda t: np.array([t, wave_func(t) + 0.3, 0]),
41
t_range=[x_start, x_end],
42
color=BLUE,
43
stroke_width=4
44
),
45
ParametricFunction(
46
lambda t: np.array([t, wave_func(t) - 0.3, 0]),
47
t_range=[x_start, x_end],
48
color=BLUE,
49
stroke_width=4
50
)
51
)
52
smn2_rna.scale(1.3)
53
54
smn2_label = Tex("\\textbf{SMN2 RNA}", font_size=32, color=BLUE).next_to(smn2_rna, UP,
buff=0.5)
,
!
55
smn2_label.shift(LEFT * 1.7 + DOWN * 1)
56
57
self.add(smn2_rna)
20
Page 20 of 30
58
self.play(Write(smn2_label), run_time=1)
59
self.wait(1)
60
61
# An error marker (red exclamation mark, with a circle around) pops on the RNA
62
exclamation_mark = Tex("!", font_size=56, color=RED)
63
error_circle = Circle(radius=0.3, color=RED, stroke_width=3)
64
error_marker = VGroup(error_circle, exclamation_mark).move_to(smn2_rna.get_center() + RIGHT *
2 + UP * 0.35)
,
!
65
error_flash = Flash(error_marker.get_center(), color=YELLOW, flash_radius=0.4,
line_stroke_width=6)
,
!
66
67
self.play(Create(error_marker), error_flash, run_time=1)
68
self.wait(1)
69
70
# two dashed lines to indicate splicing
71
splice_line1 = DashedLine(
72
start=smn2_rna[0].point_from_proportion(0.5),
73
end=smn2_rna[1].point_from_proportion(0.5),
74
color=WHITE,
75
stroke_width=4,
76
dash_length=0.06,
77
buff=0
78
)
79
splice_line2 = DashedLine(
80
start=smn2_rna[0].point_from_proportion(0.8),
81
end=smn2_rna[1].point_from_proportion(0.8),
82
color=WHITE,
83
stroke_width=4,
84
dash_length=0.06,
85
buff=0
86
)
87
exon7_text = Tex("\\textbf{Exon 7} \\\\excluded", font_size=28,
color=RED).next_to(splice_line2, RIGHT, buff=0.3)
,
!
88
exon7_text.next_to(error_marker, DOWN, buff=0.2)
89
self.play(Create(splice_line1), Create(splice_line2), Write(exon7_text), run_time=1)
90
self.wait(1)
91
92
# arrow down
93
arrow = Arrow(
94
start=splice_line1.get_bottom() + DOWN * 0.2,
95
end=splice_line1.get_bottom() + DOWN * 1.2,
96
color=YELLOW,
97
buff=0,
98
stroke_width=6
99
)
100
101
# 3/4 circle to represent truncated protein
102
truncated_protein = Arc(
103
radius=0.4,
104
start_angle=PI / 4,
105
angle=3 * PI / 2,
106
color=ORANGE,
107
stroke_width=6
108
).move_to(arrow.get_end() + DOWN * 0.5)
109
truncated_label = Tex("\\textbf{Truncated SMN Protein}", font_size=28,
color=ORANGE).next_to(truncated_protein, DOWN, buff=0.3)
,
!
110
111
self.play(
112
Create(arrow),
113
Write(truncated_label),
114
Create(truncated_protein),
115
run_time=1
116
)
117
self.wait(1)
21
Page 21 of 30
118
119
class Scene19_NusinersenTherapy(Scene):
120
def construct(self):
121
# recreate the ending state of Scene 18
122
# title
123
title = Tex("\\textbf{SMN2 Gene As a Backup}", font_size=48, color=YELLOW)
124
title.move_to(UP * 3)
125
self.add(title)
126
127
# SMN2 RNA
128
x_start = -6
129
x_end = 6
130
amplitude = 0.3
131
frequency = 1
132
wave_func = lambda x: amplitude * np.sin(frequency * x)
133
smn2_rna = VGroup(
134
ParametricFunction(
135
lambda t: np.array([t, wave_func(t) + 0.3, 0]),
136
t_range=[x_start, x_end],
137
color=BLUE,
138
stroke_width=4
139
),
140
ParametricFunction(
141
lambda t: np.array([t, wave_func(t) - 0.3, 0]),
142
t_range=[x_start, x_end],
143
color=BLUE,
144
stroke_width=4
145
)
146
)
147
smn2_rna.scale(1.3)
148
smn2_label = Tex("\\textbf{SMN2 RNA}", font_size=32, color=BLUE).next_to(smn2_rna, UP,
buff=0.5)
,
!
149
smn2_label.shift(LEFT * 1.7 + DOWN * 1)
150
self.add(smn2_rna, smn2_label)
151
152
# error marker
153
exclamation_mark = Tex("!", font_size=56, color=RED)
154
error_circle = Circle(radius=0.3, color=RED, stroke_width=3)
155
error_marker = VGroup(error_circle, exclamation_mark).move_to(smn2_rna.get_center() + RIGHT *
2 + UP * 0.35)
,
!
156
self.add(error_marker)
157
158
# splice lines
159
splice_line1 = DashedLine(
160
start=smn2_rna[0].point_from_proportion(0.5),
161
end=smn2_rna[1].point_from_proportion(0.5),
162
color=WHITE,
163
stroke_width=4,
164
dash_length=0.06,
165
buff=0
166
)
167
splice_line2 = DashedLine(
168
start=smn2_rna[0].point_from_proportion(0.8),
169
end=smn2_rna[1].point_from_proportion(0.8),
170
color=WHITE,
171
stroke_width=4,
172
dash_length=0.06,
173
buff=0
174
)
175
exon7_text = Tex("\\textbf{Exon 7} \\\\excluded", font_size=28,
color=RED).next_to(splice_line2, RIGHT, buff=0.3)
,
!
176
exon7_text.next_to(error_marker, DOWN, buff=0.2)
177
self.add(splice_line1, splice_line2, exon7_text)
178
22
Page 22 of 30
179
# arrow
180
arrow = Arrow(
181
start=splice_line1.get_bottom() + DOWN * 0.2,
182
end=splice_line1.get_bottom() + DOWN * 1.2,
183
color=YELLOW,
184
buff=0,
185
stroke_width=6
186
)
187
self.add(arrow)
188
189
# truncated protein
190
truncated_protein = Arc(
191
radius=0.4,
192
start_angle=PI / 4,
193
angle=3 * PI / 2,
194
color=ORANGE,
195
stroke_width=6
196
).move_to(arrow.get_end() + DOWN * 0.5)
197
truncated_label = Tex("\\textbf{Truncated SMN Protein}", font_size=28,
color=ORANGE).next_to(truncated_protein, DOWN, buff=0.3)
,
!
198
self.add(truncated_protein, truncated_label)
199
200
self.wait(1)
201
202
#### NEW SCENE
203
204
new_title = Tex("\\textbf{Nusinersen Therapy}", font_size=48, color=YELLOW)
205
new_title.move_to(UP * 3)
206
self.play(
207
Transform(title, new_title),
208
FadeOut(exon7_text),
209
FadeOut(splice_line1), FadeOut(splice_line2),
210
run_time=1
211
)
212
213
# Proofreader (a purple oval)
214
proofreader = Ellipse(width=1.8, height=1.3, color=PURPLE, fill_color=PURPLE,
fill_opacity=0.5, stroke_width=3)
,
!
215
proofreader_label = Tex("\\textbf{Nusinersen}", font_size=32, color=WHITE)
216
proofreader_label.move_to(proofreader.get_center())
217
proofreader_group = VGroup(proofreader, proofreader_label)
218
# move out of screen on the right
219
proofreader_group.move_to(error_marker.get_center() + RIGHT * 8 + UP * 0.5)
220
221
# animate proofreader moving to the error site
222
self.play(
223
proofreader_group.animate.move_to(error_marker.get_center() + UP * 0.5),
224
run_time=1
225
)
226
# animate proofreader fixing the error
227
self.play(
228
FadeOut(error_marker),
229
Flash(error_marker.get_center(), color=GREEN, flash_radius=0.4, line_stroke_width=6),
230
run_time=1
231
)
232
self.wait(1)
233
234
# fixed protein
235
fixed_protein = Circle(radius=0.4, color=GREEN, stroke_width=6)
236
fixed_label = Tex("\\textbf{Full-length SMN Protein}", font_size=28, color=GREEN)
237
fixed_protein.move_to(truncated_protein.get_center())
238
fixed_label.move_to(truncated_label.get_center())
239
240
# animate splicing and protein change
23
Page 23 of 30
241
self.play(
242
Transform(truncated_protein, fixed_protein),
243
Transform(truncated_label, fixed_label),
244
run_time=1
245
)
246
247
self.wait(2)
ethics.py
This le contains code for creating animations about ethical considerations in gene therapy, including historical
cases, public opinion, and regulatory concerns.
1
from manim import *
2
import random
3
4
# ETHICAL DISCUSSION SCENES
5
6
class Scene20_EthicalTitle(Scene):
7
"""Chapter Title: Ethical Considerations"""
8
def construct(self):
9
# Text animation
10
chapter = Tex("{\\scshape\\bfseries CHAPTER V}", font_size=50, color=YELLOW)
11
title = Tex("{\\bfseries Gene Therapy Ethics}", font_size=64, color=YELLOW)
12
separator = Line(start=LEFT * 3, end=RIGHT * 3, color=ORANGE, stroke_width=4)
13
14
chapter.move_to(UP * 0.75)
15
title.move_to(DOWN * 0.75)
16
separator.move_to(ORIGIN)
17
18
self.play(
19
Write(chapter, run_time=1.5),
20
Create(separator, run_time=1.5),
21
Write(title, run_time=1.5)
22
)
23
24
self.wait(3)
25
26
class Scene21_HumanWithQuestionMarks(Scene):
27
def construct(self):
28
# human svg
29
human = SVGMobject("./human_outline.svg", fill_color=BLUE, fill_opacity=0.3,
stroke_color=BLUE, stroke_width=2, should_center=True)
,
!
30
human.scale(5)
31
human.move_to(DOWN*1.5)
32
self.play(Create(human), run_time=2)
33
34
# Create question marks with different properties
35
question_marks = []
36
colors = [RED, YELLOW, GREEN, PURPLE, ORANGE, PINK, TEAL]
37
positions = [
38
DOWN * 2 + LEFT * 3,
39
UP * 3 + RIGHT * 2,
40
LEFT * 4 + UP * 1,
41
RIGHT * 4 + UP * 0.5,
42
DOWN * 2.5 + RIGHT * 4,
43
LEFT * 3.5 + UP * 3,
44
RIGHT * 3 + DOWN * 3.5,
45
LEFT * 2 + UP * 1.5,
46
RIGHT * 2.5 + UP * 2,
47
LEFT * 5 + UP * 2.5,
48
RIGHT * 5 + UP * 1.5,
24
Page 24 of 30
49
DOWN * 3.5 + LEFT * 1.5,
50
]
51
52
# Predefined sizes for each question mark
53
sizes = [65, 72, 48, 55, 78, 43, 69, 51, 76, 58, 62, 71]
54
55
for i, (pos, color, size) in enumerate(zip(positions, colors * 2, sizes)):
56
qmark = Tex("?", font_size=size, color=color)
57
qmark.move_to(pos)
58
question_marks.append(qmark)
59
60
# Fade in question marks with lag
61
self.play(
62
LaggedStart(*[FadeIn(qmark) for qmark in question_marks],
63
lag_ratio=0.5,
64
run_time=6)
65
)
66
67
# text
68
philosophical_text = Tex("$\\bullet$ Philosophical question?", font_size=50, color=WHITE)
69
medical_safety_text = Tex("$\\bullet$ Medical safety!", font_size=50, color=WHITE)
70
71
philosophical_text.move_to(DOWN * 2.6 + LEFT * 4)
72
medical_safety_text.next_to(philosophical_text, DOWN, aligned_edge=LEFT, buff=0.2)
73
74
self.play(Write(philosophical_text, run_time=1))
75
self.wait(0.5)
76
self.play(Write(medical_safety_text, run_time=1))
77
self.wait(3)
78
79
class Scene22_JesseGelsingerCaseTimeline(Scene):
80
def construct(self):
81
# Title
82
title = Tex("\\textbf{Jesse Gelsinger Case Timeline}", font_size=48, color=YELLOW)
83
title.move_to(UP * 3.5)
84
self.play(Write(title, run_time=0.5))
85
self.wait(0.5)
86
87
# Timeline arrow
88
timeline = Arrow(start=LEFT * 6 + UP * 3, end=LEFT * 6 + DOWN * 4, color=YELLOW,
stroke_width=4)
,
!
89
self.play(Create(timeline), run_time=0.5)
90
self.wait(0.5)
91
92
# Events
93
events = [
94
("{\\bfseries 18 Jun 1981:}", "Jesse Gelsinger born, later diagnosed with OTC
deficiency"),
,
!
95
("{\\bfseries 13 Sept 1999:}", "At 18, Gelsinger injected with experimental gene
therapy"),
,
!
96
("{\\bfseries 17 Sept 1999:}", "Gelsinger died from organ failure due to immune
response"),
,
!
97
]
98
99
for i, event_text in enumerate(events):
100
event = VGroup(
101
Tex(event_text[0], font_size=28, color=WHITE),
102
Tex(event_text[1], font_size=32, color=WHITE)
103
)
104
event.arrange(DOWN, aligned_edge=LEFT)
105
x_pos = LEFT * 6
106
y_pos = UP * 2 + (DOWN * 4) * (i / (len(events) - 1))
107
marker = Dot(point=x_pos + y_pos, color=RED, radius=0.1)
108
event.next_to(marker, RIGHT, buff=0.3)
25
Page 25 of 30
109
self.play(Create(marker), Write(event, run_time=1))
110
self.wait(0.5)
111
112
self.wait(3)
113
114
class Scene23_BubbleBoy(Scene):
115
def construct(self):
116
# Create 4 stick figures in blue bubbles arranged in 2x2 grid
117
stick_figures = []
118
bubbles = []
119
120
# Positions for 2x2 grid
121
positions = [
122
UP * 1.5 + LEFT * 2,
# Top left
123
UP * 1.5 + RIGHT * 2,
# Top right
124
DOWN * 1.5 + LEFT * 2,
# Bottom left
125
DOWN * 1.5 + RIGHT * 2
# Bottom right
126
]
127
128
for pos in positions:
129
# Create stick figure
130
stick = VGroup(
131
Circle(radius=0.15, color=WHITE, fill_opacity=1),
# Head
132
Line(start=UP * 0.25, end=DOWN * 0.5, color=WHITE),
# Body
133
Line(start=UP * 0.25, end=DOWN * 0.15 + LEFT * 0.25, color=WHITE),
# Left arm
134
Line(start=UP * 0.25, end=DOWN * 0.15 + RIGHT * 0.25, color=WHITE),
# Right arm
135
Line(start=DOWN * 0.5, end=DOWN * 0.8 + LEFT * 0.2, color=WHITE),
# Left leg
136
Line(start=DOWN * 0.5, end=DOWN * 0.8 + RIGHT * 0.2, color=WHITE),
# Right leg
137
)
138
stick[0].move_to(UP * 0.4)
139
stick.scale(0.8)
140
stick.move_to(pos)
141
142
# Create bubble
143
bubble = Circle(radius=1.2, color=BLUE, stroke_width=4, fill_opacity=0.3, fill_color=BLUE)
144
bubble.move_to(pos)
145
146
stick_figures.append(stick)
147
bubbles.append(bubble)
148
149
# Show all stick figures and blue bubbles
150
self.play(
151
*[Create(bubble) for bubble in bubbles],
152
*[Create(stick) for stick in stick_figures],
153
run_time=1
154
)
155
self.wait(0.5)
156
157
# Change colors: bottom right to red, others to green
158
# Also create warning text for bottom right
159
warning_text = Tex("Accidental activation\\\\ of leukaemia (25\\%)", font_size=32, color=RED)
160
warning_text.next_to(bubbles[3], DOWN, buff=0.2)
161
162
self.play(
163
bubbles[3].animate.set_color(RED),
# Bottom right to red
164
*[bubbles[i].animate.set_color(GREEN) for i in range(3)],
# Others to green
165
Write(warning_text),
166
run_time=1
167
)
168
169
self.wait(3)
170
171
class Scene24_ImmuneToGeneTherapy(Scene):
26
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172
"""Scene showing immune response to gene therapy"""
173
def construct(self):
174
# 1. Create green human outline on the right half
175
human = SVGMobject("./human_outline.svg", fill_color=GREEN, fill_opacity=0.3,
stroke_color=GREEN, stroke_width=3, should_center=True)
,
!
176
human.scale(3)
177
human.move_to(RIGHT * 3)
178
179
# Create AAV viral vector with RNA strand (upper-left)
180
aav_capsid = RegularPolygon(n=6, radius=1.2, color=PURPLE, stroke_width=4, fill_color=PURPLE,
fill_opacity=0.2)
,
!
181
182
spike_positions = [
183
UP * 1.2,
184
UP * 0.6 + RIGHT * 1.0,
185
DOWN * 0.6 + RIGHT * 1.0,
186
DOWN * 1.2,
187
DOWN * 0.6 + LEFT * 1.0,
188
UP * 0.6 + LEFT * 1.0
189
]
190
191
spikes = VGroup()
192
for pos in spike_positions:
193
spike = Triangle(color=PURPLE, fill_color=PURPLE, fill_opacity=0.8)
194
spike.scale(0.15)
195
spike.move_to(pos)
196
angle = np.arctan2(pos[1], pos[0])
197
spike.rotate(angle + PI/2)
198
spikes.add(spike)
199
200
# RNA strand inside
201
rna_strand = ParametricFunction(
202
lambda t: np.array([
203
0.2 * np.sin(4 * PI * t),
204
1.5 * t - 0.75,
205
0
206
]),
207
t_range=[0, 1],
208
color=GREEN,
209
stroke_width=6
210
).scale(0.3)
211
212
aav_capsid.scale(0.5)
213
spikes.scale(0.5)
214
aav_vector = VGroup(aav_capsid, spikes, rna_strand)
215
aav_vector.move_to(UP * 2 + LEFT * 4)
216
217
# Create CRISPR-Cas9 protein (lower-left)
218
crispr_cas9 = VGroup(
219
Rectangle(width=1.5, height=0.6, color=BLUE, fill_color=BLUE, fill_opacity=0.5),
220
Tex("\\textbf{CRISPR-\\\\Cas9}", font_size=20, color=BLUE)
221
)
222
crispr_cas9.scale(1.4)
223
crispr_cas9[1].move_to(crispr_cas9[0].get_center())
224
crispr_cas9.move_to(DOWN * 2 + LEFT * 4)
225
226
# Display all elements
227
self.play(
228
Create(human),
229
Create(aav_vector),
230
Create(crispr_cas9),
231
run_time=1
232
)
233
self.wait(1)
27
Page 27 of 30
234
235
# 2. Vector approaches human but is bounced back
236
target_pos = human.get_left() + LEFT * 0.5
237
self.play(
238
aav_vector.animate.move_to(target_pos),
239
run_time=1
240
)
241
# self.wait(0.3)
242
243
# Bounce back with shake
244
self.play(
245
aav_vector.animate.shift(LEFT * 0.3),
246
run_time=0.2
247
)
248
# self.play(
249
# aav_vector.animate.shift(LEFT * 1.5),
250
# run_time=0.8,
251
# rate_func=smooth
252
# )
253
self.wait(0.5)
254
255
# 3. Red cross forms on vector and it turns gray
256
cross_line1 = Line(
257
start=UP * 0.5 + LEFT * 0.5,
258
end=DOWN * 0.5 + RIGHT * 0.5,
259
color=RED,
260
stroke_width=8
261
)
262
cross_line2 = Line(
263
start=UP * 0.5 + RIGHT * 0.5,
264
end=DOWN * 0.5 + LEFT * 0.5,
265
color=RED,
266
stroke_width=8
267
)
268
red_cross_vector = VGroup(cross_line1, cross_line2)
269
red_cross_vector.move_to(aav_vector.get_center())
270
271
self.play(
272
Create(red_cross_vector),
273
aav_capsid.animate.set_color(GRAY),
274
aav_capsid.animate.set_fill(GRAY, opacity=0.2),
275
*[spike.animate.set_color(GRAY).set_fill(GRAY, opacity=0.2) for spike in spikes],
276
aav_vector.animate.set_stroke(GRAY),
277
rna_strand.animate.set_color(GRAY),
278
run_time=1
279
)
280
self.wait(1)
281
282
# 4. CRISPR-Cas9 enters the human
283
self.play(
284
crispr_cas9.animate.move_to(human.get_center()),
285
run_time=2
286
)
287
self.wait(0.5)
288
289
# Cross forms on human and human turns gray
290
cross_line3 = Line(
291
start=UP * 1.5 + LEFT * 1.5,
292
end=DOWN * 1.5 + RIGHT * 1.5,
293
color=RED,
294
stroke_width=10
295
)
296
cross_line4 = Line(
28
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297
start=UP * 1.5 + RIGHT * 1.5,
298
end=DOWN * 1.5 + LEFT * 1.5,
299
color=RED,
300
stroke_width=10
301
)
302
red_cross_human = VGroup(cross_line3, cross_line4)
303
red_cross_human.move_to(human.get_center())
304
305
self.play(
306
Create(red_cross_human),
307
human.animate.set_color(GRAY).set_fill(GRAY, opacity=0.3),
308
crispr_cas9.animate.set_color(GRAY).set_opacity(0.3),
309
run_time=1.5
310
)
311
self.wait(2)
312
313
class Scene25_PublicOpinionSurvey(Scene):
314
"""Public opinion survey on gene therapy"""
315
def construct(self):
316
# Title
317
title = Tex("\\textbf{Public Opinion Survey}", font_size=48, color=YELLOW)
318
title.move_to(UP * 3.2)
319
320
# Create 100 people icons in 10x10 grid
321
people_icons = VGroup()
322
rows, cols = 10, 10
323
spacing = 0.6
324
325
for row in range(rows):
326
for col in range(cols):
327
person = Circle(radius=0.08, color=WHITE, fill_opacity=1, fill_color=WHITE)
328
person[0].move_to(UP * 0.1)
329
330
x_pos = (col - cols / 2) * spacing + spacing / 2
331
y_pos = (rows / 2 - row) * spacing - spacing / 2
332
person.move_to(RIGHT * x_pos + UP * y_pos + DOWN * 0.5)
333
334
people_icons.add(person)
335
336
self.play(
337
Write(title),
338
LaggedStart(*[FadeIn(person) for person in people_icons], lag_ratio=0.01),
339
run_time=1
340
)
341
self.wait(1)
342
343
# Group them randomly (predefined random)
344
oppose_indices = (
345
2, 5, 8, 13, 14, 19, 20, 23, 27, 28,
346
30, 42, 45, 47, 50, 51, 52, 60, 63, 68,
347
69, 94, 97, 99, 92
348
)
349
oppose_people = [people_icons[i] for i in oppose_indices]
350
support_people = [people_icons[i] for i in range(100) if i not in oppose_indices]
351
352
# Highlight 75% in green (supporting gene therapy)
353
support_label = Tex("\\textbf{75\\% believe in\\\\gene therapy}", font_size=48, color=GREEN)
354
support_label.move_to(LEFT * 5)
355
356
self.play(
357
*[support_people[i].animate.set_color(GREEN) for i in range(75)],
358
Write(support_label),
359
run_time=1
29
Page 29 of 30
360
)
361
self.wait(0.5)
362
363
# Show the remaining 25% in red
364
oppose_label = Tex("\\textbf{25\\% uncertain\\\\or opposed}", font_size=48, color=RED)
365
oppose_label.move_to(RIGHT * 5)
366
367
self.play(
368
*[oppose_people[i].animate.set_color(RED) for i in range(25)],
369
Write(oppose_label),
370
run_time=1
371
)
372
373
self.wait(3)
374
375
class Scene26_EthicalConcerns(Scene):
376
"""Ethical concerns about gene therapy"""
377
def construct(self):
378
# Title
379
title = Tex("{\\bfseries Ethical Concerns}", font_size=56, color=YELLOW)
380
title.move_to(UP * 3)
381
382
# Concern statements
383
concern1_title = Tex("$\\bullet$ \\textbf{Playing God}", font_size=36, color=RED)
384
concern1_detail = Tex("Changing nature may cause unexpected dangerous results", font_size=28)
385
concern1 = VGroup(concern1_title, concern1_detail).arrange(DOWN, buff=0.2, aligned_edge=LEFT)
386
387
concern2_title = Tex("$\\bullet$ \\textbf{Fairness and Access}", font_size=36, color=ORANGE)
388
concern2_detail = Tex("Treatments cost millions, risking a permanent genetic divide",
font_size=28)
,
!
389
concern2 = VGroup(concern2_title, concern2_detail).arrange(DOWN, buff=0.2, aligned_edge=LEFT)
390
391
concern3_title = Tex("$\\bullet$ \\textbf{Threat to Human Identity}", font_size=36,
color=PURPLE)
,
!
392
concern3_detail = Tex("Brain-editing errors could cause catastrophic damage", font_size=28)
393
concern3 = VGroup(concern3_title, concern3_detail).arrange(DOWN, buff=0.2, aligned_edge=LEFT)
394
395
concerns = VGroup(concern1, concern2, concern3).arrange(DOWN, buff=0.7, aligned_edge=LEFT)
396
concerns.move_to(DOWN * 0.3)
397
398
# Animate title
399
self.play(Write(title), run_time=1)
400
self.wait(0.5)
401
402
# Animate concerns appearing one by one
403
self.play(FadeIn(concern1, shift=UP * 0.3), run_time=1)
404
self.wait(0.5)
405
self.play(FadeIn(concern2, shift=UP * 0.3), run_time=1)
406
self.wait(0.5)
407
self.play(FadeIn(concern3, shift=UP * 0.3), run_time=1)
408
409
self.wait(3)
410
30
Page 30 of 30
See also
-
CCCH9044-Individual-Essay
The 3000-word individual essay for the course CCCH9044.
-
CCGL9042-Question-Bank
The question bank for CCGL9042 in-class quizzes.
-
CCHU9094-Essay
Read the student submission of the essay to CCHU9094. This work has been graded A.
-
COMP1110-Project
The GitHub repository of the group project.
-
COMP1110-Project-IndividualReport_JacobShing
Individual report for COMP1110 (25/26 Spring) by Jacob Shing.
-
COMP1110-Project-Plan
The project plan for COMP1110 (25/26 Spring).