Maria Castellanos
commited on
Commit
Β·
9638dbd
1
Parent(s):
0c194f3
Improve About
Browse files- _static/challenge_logo.png +0 -0
- app.py +38 -10
_static/challenge_logo.png
ADDED
|
app.py
CHANGED
|
@@ -48,21 +48,49 @@ def gradio_interface():
|
|
| 48 |
timer.tick(fn=update_current_dataframe, inputs=[data_version], outputs=data_version)
|
| 49 |
|
| 50 |
### Header
|
| 51 |
-
gr.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 52 |
|
| 53 |
# --- Welcome markdown message ---
|
| 54 |
welcome_md = """
|
| 55 |
# π OpenADMET + XXX
|
| 56 |
## Computational Blind Challenge in ADMET
|
| 57 |
|
| 58 |
-
|
| 59 |
-
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 60 |
|
| 61 |
-
|
|
|
|
|
|
|
| 62 |
|
| 63 |
-
|
| 64 |
-
*Absorption*, *Distribution*, *Metabolism*, *Excretion*, *Toxicology*--or **ADMET**--endpoints sit in the middle of the assay cascade and can make or break preclinical candidate molecules.
|
| 65 |
-
For this blind challenge we selected several crucial endpoints for the community to predict:
|
| 66 |
- LogD
|
| 67 |
- Kinetic Solubility **KSOL**: uM
|
| 68 |
- Mouse Liver Microsomal (**MLM**) *CLint*: mL/min/kg
|
|
@@ -126,10 +154,10 @@ def gradio_interface():
|
|
| 126 |
with gr.Tabs(elem_classes="tab-buttons"):
|
| 127 |
lboard_dict = {}
|
| 128 |
|
| 129 |
-
with gr.TabItem("
|
| 130 |
gr.Markdown(welcome_md)
|
| 131 |
|
| 132 |
-
with gr.TabItem("πLeaderboard", elem_id="lb_subtabs"):
|
| 133 |
gr.Markdown("View the leaderboard for each ADMET endpoint by selecting the appropiate tab.")
|
| 134 |
# Make separate leaderboards in separate tabs
|
| 135 |
#per_ep = build_leaderboard()
|
|
@@ -162,7 +190,7 @@ def gradio_interface():
|
|
| 162 |
|
| 163 |
data_version.change(fn=refresh_if_changed, outputs=[lboard_dict[ep] for ep in ALL_EPS])
|
| 164 |
|
| 165 |
-
with gr.TabItem("Submit
|
| 166 |
gr.Markdown(
|
| 167 |
"""
|
| 168 |
# ADMET Endpoints Submission
|
|
|
|
| 48 |
timer.tick(fn=update_current_dataframe, inputs=[data_version], outputs=data_version)
|
| 49 |
|
| 50 |
### Header
|
| 51 |
+
with gr.Row():
|
| 52 |
+
with gr.Column(scale=8): # bigger text area
|
| 53 |
+
gr.Markdown("""
|
| 54 |
+
## Welcome to the OpenADMET + XXX Blind Challenge!
|
| 55 |
+
Your task is to develop and submit predictive models for key ADMET properties on a blinded test set of real world drug discovery data π§βπ¬
|
| 56 |
+
|
| 57 |
+
Go to the **Leaderboard** to check out how the challenge is going.
|
| 58 |
+
To participate, head out to the **Submit** tab and upload your results as a `CSV` file.
|
| 59 |
+
"""
|
| 60 |
+
)
|
| 61 |
+
with gr.Column(scale=1): # smaller side column for logo
|
| 62 |
+
gr.Image(
|
| 63 |
+
value="./_static/challenge_logo.png",
|
| 64 |
+
show_label=False,
|
| 65 |
+
show_download_button=False,
|
| 66 |
+
width="10vw", # Take up the width of the column (2/8 = 1/4)
|
| 67 |
+
)
|
| 68 |
|
| 69 |
# --- Welcome markdown message ---
|
| 70 |
welcome_md = """
|
| 71 |
# π OpenADMET + XXX
|
| 72 |
## Computational Blind Challenge in ADMET
|
| 73 |
|
| 74 |
+
This challenge is a community-driven initiative to benchmark predictive models for ADMET properties in drug discovery,
|
| 75 |
+
hosted by **OpenADMET** in collaboration with **XXX**.
|
| 76 |
+
|
| 77 |
+
|
| 78 |
+
## Why are ADMET properties important in drug discovery?
|
| 79 |
+
Small molecules continue to be the bricks and mortar of drug discovery globally, accounting for ~75% of FDA approvals over the last decade.
|
| 80 |
+
Oral bioavailability, easily tunable properties, modulation of a wide range of mechanisms,
|
| 81 |
+
and ease of manufacturing make small molecules highly attractive as therapeutic agents, a trend that is not expected to drastically change,
|
| 82 |
+
despite increased interest in biologics. Indeed, newer small molecule modalities such as degraders, molecular glues, and antibody-drug conjugates
|
| 83 |
+
(to name a few) make understanding small molecule properties more important than ever.
|
| 84 |
+
|
| 85 |
+
It is fairly difficult to predict the lifetime and distribution of small molecules within the body. Additionally,
|
| 86 |
+
interaction with off-targets can cause safety issues and toxicity. Collectively these *Absorption*, *Distribution*, *Metabolism*, *Excretion*, *Toxicology*--or **ADMET**--properties
|
| 87 |
+
sit in the middle of the assay cascade and can make or break preclinical candidate molecules.
|
| 88 |
|
| 89 |
+
**OpenADMET** aims to address these challenges through an open science effort to build predictive models of ADMET properties by characterizing the proteins and mechanisms
|
| 90 |
+
that give rise to these properties through integrated structural biology, high throughput experimentation and integrative computational models.
|
| 91 |
+
Read more about our strategy to transform drug discovery on our [website](https://openadmet.org/community/blogs/whatisopenadmet/).
|
| 92 |
|
| 93 |
+
For this blind challenge we selected ten (10) crucial endpoints for the community to predict:
|
|
|
|
|
|
|
| 94 |
- LogD
|
| 95 |
- Kinetic Solubility **KSOL**: uM
|
| 96 |
- Mouse Liver Microsomal (**MLM**) *CLint*: mL/min/kg
|
|
|
|
| 154 |
with gr.Tabs(elem_classes="tab-buttons"):
|
| 155 |
lboard_dict = {}
|
| 156 |
|
| 157 |
+
with gr.TabItem("π About"):
|
| 158 |
gr.Markdown(welcome_md)
|
| 159 |
|
| 160 |
+
with gr.TabItem("π Leaderboard", elem_id="lb_subtabs"):
|
| 161 |
gr.Markdown("View the leaderboard for each ADMET endpoint by selecting the appropiate tab.")
|
| 162 |
# Make separate leaderboards in separate tabs
|
| 163 |
#per_ep = build_leaderboard()
|
|
|
|
| 190 |
|
| 191 |
data_version.change(fn=refresh_if_changed, outputs=[lboard_dict[ep] for ep in ALL_EPS])
|
| 192 |
|
| 193 |
+
with gr.TabItem("βοΈ Submit"):
|
| 194 |
gr.Markdown(
|
| 195 |
"""
|
| 196 |
# ADMET Endpoints Submission
|