diff --git a/.gitignore b/.gitignore
index 22ad3a9..3d50c62 100644
--- a/.gitignore
+++ b/.gitignore
@@ -897,3 +897,6 @@ FodyWeavers.xsd
# PyPi file
.pypirc
+*.json
+*.csv
+*.ipynb
\ No newline at end of file
diff --git a/Main.py b/Main.py
index ff7c15b..efb3a60 100644
--- a/Main.py
+++ b/Main.py
@@ -5,6 +5,7 @@
import streamlit as st
import base64
from streamlit_card import card
+from st_social_media_links import SocialMediaIcons
st.set_page_config(
layout="wide",
@@ -28,6 +29,7 @@
padding-right: 5rem;
}
.stTabs [data-baseweb="tab-list"] button [data-testid="stMarkdownContainer"] p {font-size:1.3rem;}
+ [data-testid="stExpander"] details:hover summary{background-color: #d0e9e2;}
""",
unsafe_allow_html=True,
@@ -49,6 +51,13 @@ def load_logo(filepath):
return data
+def img_to_html(img_path):
+ img_html = "
".format(
+ load_logo(img_path)
+ )
+ return img_html
+
+
tab1, tab2, tab3, tab4 = st.tabs(["About", "Tools", "Publications", "Team"])
with tab1:
@@ -103,8 +112,8 @@ def load_logo(filepath):
Project overview:
- Start year: 2021
- - End year: 2024
- - Grant agreement ID: 03ZU1109KB
+ - End year: 2027 (including 2nd phase)
+ - Grant agreement ID: 03ZU1109KB (InnoDATA)
- Funding: 14M€
- Funding source: Federal Ministry of Education and Research (BMBF)
"""
@@ -148,21 +157,22 @@ def load_logo(filepath):
# tools tab
with tab2:
- st.markdown("### Knowledge Graph")
- with st.expander(label="Graph based tools"):
+ st.markdown("### Explore our tools and workflows")
+ with st.expander(label=r"$\textsf{\Large Dashboards and Databases}$"):
col1, col2, col3 = st.columns(3)
with col1:
hasClicked = card(
title="R4A Expertise Dashboard",
text="Dashboard for the the REMEDi4ALL expertise knowledge graph",
- image=load_logo("images/r4a_logo.png"),
+ image=load_logo("images/app_logos/r4a_logo.png"),
url="https://r4a-expertise-dashboard.serve.scilifelab.se/",
styles={
"card": {
"border-radius": "10px",
- "box-shadow": "0 0 10px rgba(0,0,0,0.5)",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
}
},
)
@@ -171,113 +181,191 @@ def load_logo(filepath):
hasClicked = card(
title="KGG",
text="Automated workflow for disease-specific KGs",
- image=load_logo("images/kg_2.png"),
- url="/KGGapp",
+ image=load_logo("images/app_logos/kgg.png"),
+ url="/KG_Generator",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col3:
hasClicked = card(
title="AntiMicrobial KG",
text="Data warehouse of experimentally validated antibacterial chemicals",
- image=load_logo("images/antimicrobial.webp"),
+ image=load_logo("images/app_logos/antimicrobial.webp"),
url="https://antimicrobial-kg.serve.scilifelab.se/",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
+ )
+
+ col4, col5, col6 = st.columns(3)
+
+ with col4:
+ hasClicked = card(
+ title="PROTACKB",
+ text="A comprehensive knowledgebase of PROTACs, molecular glues and degraders",
+ image=load_logo("images/app_logos/ar_demo.png"),
+ url="/PROTAC-KB",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
- st.markdown("### Machine learning models")
+ with col5:
+ hasClicked = card(
+ title="PROXIDRUGS",
+ text="Dashboard for sub-projects in PROXIDRUGS",
+ image=load_logo("images/app_logos/proxidrugs.PNG"),
+ url="/Proxidrugs",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
+ )
- with st.expander(label="ML models"):
+ with st.expander(label=r"$\textsf{\Large Machine learning models}$"):
col1, col2, col3 = st.columns(3)
with col1:
hasClicked = card(
title="AntiMicrobial Model",
text="Model for predicting antimicorbial activity of small molecules",
- image=load_logo("images/antimicrobial.webp"),
+ image=load_logo("images/app_logos/antimicrobial.webp"),
url="https://antimicrobial-kg.serve.scilifelab.se/Model_Prediction",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col2:
hasClicked = card(
title="E3 Ligase Model",
- text="Model for predicting speicificity of E3 ligase binders",
- image=load_logo("images/protac.webp"),
+ text="Model for predicting specificity of E3 ligase binders",
+ image=load_logo("images/app_logos/protac.webp"),
url="https://github.com/Fraunhofer-ITMP/E3_binder_Model",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
- st.markdown("### Screening data preprocessing")
-
- with st.expander("Preprocessing tools"):
+ with st.expander(label=r"$\textsf{\Large Screening data preprocessing tools}$"):
col1, col2, col3 = st.columns(3)
with col1:
card(
title="Dose-Response Analyses",
text="Fit dose-response curves from normalised biochemical assay data",
- image=load_logo("images/drc.png"),
+ image=load_logo("images/app_logos/drc.png"),
url="https://hub.knime.com/fraunhoferitmp/spaces/Public/Dose_Response_Biochemical/DRCfit_biochemical_ECBD~6NLZB5Jkgn6j5a6Y/current-state",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col2:
hasClicked = card(
title="Chemical annotator",
text="Annotation of chemicals with biochemical and pharmaceutical information retrieved from ChEMBL",
- image=load_logo("images/workflow.png"),
+ image=load_logo("images/app_logos/workflow.png"),
url="https://hub.knime.com/fraunhoferitmp/spaces/Public/Remedi4All/R4A_AnnotationTool_v1~RPNHTYMP7vUEoUwD/current-state",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col3:
hasClicked = card(
- title="Annotator Dashboard",
- text="Dashboard of biochemical and pharmaceutical information retrieved from ChEMBL",
- image=load_logo("images/workflow.png"),
- url="https://hub.knime.com/fraunhoferitmp/spaces/Public/Remedi4All/ChemblAssays~yQeFQzSCx6DSlZPd/current-state",
- )
-
- col1, col2, col3 = st.columns(3)
-
- with col1:
- hasClicked = card(
- title="Pareto Hit Analysis App",
- text="Some description",
- image=load_logo("images/pareto_front.png"),
- url="/Paretoapp",
- )
-
- with col2:
- hasClicked = card(
- title="ENSEMBL Gene Annotator App",
- text="Some description",
- image=load_logo("images/gene_icon.png"),
- url="/Ensemblapp",
+ title="CBDREGNum Generator",
+ text="Prepare data for submission in PROXIDRUGSDB",
+ image=load_logo("images/app_logos/cbdr.png"),
+ url="/CBDReg_Generator",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
- st.markdown("### Programming tools and workflows")
-
- with st.expander("Program tools"):
+ with st.expander(label=r"$\textsf{\Large Tools and workflows}$"):
col1, col2, col3 = st.columns(3)
with col1:
card(
title="Patent Enrichment Tool PEMT",
text="Python package for extracting patent for genes and compounds",
- image=load_logo("images/pemt.jpg"),
+ image=load_logo("images/app_logos/pemt.jpg"),
url="https://github.com/Fraunhofer-ITMP/PEMT",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col2:
card(
title="rSASC",
text="R tool for Synthetic cohorts generator for longitudinal observational patient cohorts",
- image=load_logo("images/sasc.webp"),
+ image=load_logo("images/app_logos/sasc.webp"),
url="https://github.com/Fraunhofer-ITMP/SASC",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col3:
card(
title="ALISTER",
text="Application for lipid stability evaluation",
- image=load_logo("images/alister.png"),
+ image=load_logo("images/app_logos/alister.png"),
url="https://itmp.shinyapps.io/alister/",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
col1, col2, col3 = st.columns(3)
@@ -286,33 +374,63 @@ def load_logo(filepath):
card(
title="PySASC",
text="Python tool for Synthetic cohorts generator for longitudinal observational patient cohorts",
- image=load_logo("images/sasc.webp"),
+ image=load_logo("images/app_logos/sasc.webp"),
url="https://github.com/Fraunhofer-ITMP/PySASC",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
- # with col3:
- # card(
- # title="ALISTER",
- # text="Application for lipid stability evaluation",
- # image=load_logo("images/alister.png"),
- # url="https://itmp.shinyapps.io/alister/",
- # )
+ with col2:
+ hasClicked = card(
+ title="Data Processor",
+ text="Small toolkit for processing proteins",
+ image=load_logo("images/pages/pareto_front.png"),
+ url="/Small_helper_apps",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
+ )
- st.markdown("### Findable, Accessible, Reusable, Interoperable (FAIR) data tools")
+ with col3:
+ hasClicked = card(
+ title="Chemical space visualizer",
+ text="Chemical space visualizer through t-SNE and UMAP",
+ image=load_logo("images/app_logos/umap.png"),
+ url="/Compound_space_visualizer",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
+ )
- with st.expander(label="Endorsed FAIR tools"):
+ with st.expander(
+ label=r"$\textsf{\Large Findable, Accessible, Reusable, Interoperable (FAIR) endorsed tools}$"
+ ):
col1, col2, col3 = st.columns(3)
with col1:
card(
title="FAIR Cookbook",
- text="Resource for the Life Sciences with recipes that help you to make and keep data FAIR",
- image=load_logo("images/faircookbook.png"),
+ text="Resource for the life sciences recipes that help you to make and keep data FAIR",
+ image=load_logo("images/app_logos/faircookbook.png"),
url="https://faircookbook.elixir-europe.org/",
styles={
"card": {
"border-radius": "10px",
- "box-shadow": "0 0 10px rgba(0,0,0,0.5)",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
}
},
)
@@ -321,18 +439,60 @@ def load_logo(filepath):
card(
title="FAIRplus DSM",
text="Tool to assess the FAIRness level of datasests",
- image=load_logo("images/fairplus_dsm.png"),
+ image=load_logo("images/app_logos/fairplus_dsm.png"),
url="https://fairdsm.biospeak.solutions/",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
with col3:
card(
title="FAIRSharing.org",
text="Resource on data and metadata standards, inter-related to databases and data policies",
- image=load_logo("images/fairsharing.jpg"),
+ image=load_logo("images/app_logos/fairsharing.jpg"),
url="https://fairsharing.org/",
+ styles={
+ "card": {
+ "border-radius": "10px",
+ "box-shadow": "0 0 4px rgba(0,0,0,0.5)",
+ "margin": "0px",
+ }
+ },
)
+ col1, col2, col3, col4, col5, col6, col7, col8 = st.columns(8)
+
+ col1.markdown("Find us on:")
+
+ col2.markdown(
+ f"""**LinkedIn**""",
+ unsafe_allow_html=True,
+ )
+
+ col3.markdown(
+ f"""**GitHub**""",
+ unsafe_allow_html=True,
+ )
+
+ col4.markdown(
+ f"""**X**""",
+ unsafe_allow_html=True,
+ )
+
+ col5.markdown(
+ f"""**Zenodo**""",
+ unsafe_allow_html=True,
+ )
+
+ col6.markdown(
+ f"""**KINMEHub**""",
+ unsafe_allow_html=True,
+ )
# publications tab
with tab3:
@@ -358,10 +518,32 @@ def load_logo(filepath):
)
member_df = pd.read_csv("data/members.csv")
+ active_members = member_df[member_df["alumni"] == "no"]
+ alumni_members = member_df[member_df["alumni"] == "yes"]
+
+ member_chunk_df1 = [
+ active_members[i : i + 3] for i in range(0, len(active_members), 3)
+ ]
+ member_chunk_df2 = [
+ alumni_members[i : i + 3] for i in range(0, len(alumni_members), 3)
+ ]
+
+ # Current members
+ st.header("Current members", divider="grey")
+ for sub_df in member_chunk_df1:
+ sub_df.reset_index(drop=True, inplace=True)
+ columns = st.columns(3)
+ for i, row in sub_df.iterrows():
+ with columns[i]:
+ st.write(f"### {row['member_name']}")
+ st.markdown(
+ f"**Email**: {row['member_email']}
**ORCID**: https://orcid.org/{row['member_orcid']}",
+ unsafe_allow_html=True,
+ )
- member_chunk_df = [member_df[i : i + 3] for i in range(0, len(member_df), 3)]
-
- for sub_df in member_chunk_df:
+ # Alumni members
+ st.header(":orange[Alumni members]", divider="grey")
+ for sub_df in member_chunk_df2:
sub_df.reset_index(drop=True, inplace=True)
columns = st.columns(3)
for i, row in sub_df.iterrows():
@@ -372,6 +554,8 @@ def load_logo(filepath):
unsafe_allow_html=True,
)
+ st.image("./images/clinical_ds.png", use_column_width=True)
+
# footer with text and green background
st.markdown(
"