Skip to content

Commit ddbaefd

Browse files
AhmadAlkhanAhmadAlkhan
authored
Merge pull request #19 from CompOnco/jerrysbranch
 design: Modernize website with new UI components
2 parents 3d636f1 + 1a0d4a2 commit ddbaefd

17 files changed

+3464
-348
lines changed

‎Collaborate.qmd

+502-27
Large diffs are not rendered by default.

‎Projects/GDI.qmd

+373-45
Large diffs are not rendered by default.

‎Projects/bioconductor.qmd

+196-29
Original file line numberDiff line numberDiff line change
@@ -1,43 +1,210 @@
11
---
2-
title: "Bioconductor: Open Source Software for Genomics"
3-
description: Providing Bioconductor training by redeveloping the website and developing global infrastructure to deliver high quality community-led training in local languages.
4-
about:
5-
template: solana
6-
image: "../contents/logo/bioconductor_logo_cmyk.svg"
7-
image-width: 10em
8-
links:
9-
- icon: twitter
10-
text: twitter
11-
href: https://twitter.com/bioconductor
12-
- icon: github
13-
text: Github
14-
href: https://github.com/bioconductor
15-
- icon: house-door
16-
text: Website
17-
href: https://www.bioconductor.org
18-
card_style: "summary_large_image"
19-
categories:
20-
- Genomics
21-
- Bioconductor
22-
- Community
23-
- Open Source
2+
page-layout: full
3+
format:
4+
html:
5+
html-math-method: katex
246
bibliography: references.bib
257
---
268

27-
![Bioconductor](../contents/logo/bioconductor_logo_cmyk.svg){width="508"}
9+
<style>
10+
/* Modern Bioconductor Page Styling */
11+
:root {
12+
--primary-color: #0a2463;
13+
--secondary-color: #3e92cc;
14+
--accent-color: #d81159;
15+
--light-bg: #f8f9fa;
16+
--card-bg: #ffffff;
17+
--text-primary: #1a1a2e;
18+
--text-secondary: #4a4e69;
19+
--text-light: #6c757d;
20+
--shadow: 0 10px 30px rgba(0, 0, 0, 0.08);
21+
--border-color: #e9ecef;
22+
--radius: 8px;
23+
--transition: all 0.3s ease;
24+
}
2825

29-
[Bioconductor](www.bioconductor.org) is an open source, open development software project in the R statistical software language and is widely used in bioinformatics, immunology, microbiology and single-cell genomics. Over 1200 developers have contributed software that is downloaded by users over 500K times per year.
26+
body {
27+
font-family: system-ui, -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
28+
line-height: 1.6;
29+
background-color: var(--light-bg);
30+
color: var(--text-primary);
31+
margin: 0;
32+
padding: 0;
33+
}
3034

31-
In April 2020, we established a Community Advisory Board (CAB) that includes elected representatives from America, Europe, Africa, Asia and Latin America to outreach to the growing global Bioconductor community. The CAB identified accessible high-quality training materials and delivery methods as an urgent, impactful need. Fundamental components for a successful training platform include skilled and effective program management, excellence in instruction, quality of training materials and equity in access. This proposal will redevelop the Bioconductor web presence to ensure Bioconductor communities have equitable access to quality, well-structured, project information and training materials. This work will also deliver structured, high-quality, culturally-aware, inclusive global training by developing a platform for community led instruction.
35+
/* Hero section */
36+
.hero-section {
37+
background: var(--card-bg);
38+
padding: 4rem 1rem;
39+
text-align: center;
40+
margin-bottom: 1rem;
41+
position: relative;
42+
overflow: hidden;
43+
}
3244

33-
@Reimers2006
45+
.hero-section::before {
46+
content: '';
47+
position: absolute;
48+
top: 0;
49+
left: 0;
50+
right: 0;
51+
height: 4px;
52+
background: linear-gradient(90deg, var(--secondary-color), var(--accent-color));
53+
}
3454

35-
Our lab support open source bioinformatics community and are working with European Infrastructure for life-science information ([ELIXIR](https://elixir-europe.org)) and [LERO](https://lero.ie)'s open source office.
55+
.hero-section img {
56+
width: 300px;
57+
height: auto;
58+
margin-bottom: 1.5rem;
59+
}
3660

37-
![![ELIXIR](../contents/logo/Elixir_logo-3927606181.png){alt="ELIXIR" width="147"}](../contents/logo/lero.png){width="202"}
61+
.hero-section h1 {
62+
font-size: 2.5rem;
63+
font-weight: 700;
64+
color: var(--primary-color);
65+
margin-bottom: 1rem;
66+
}
3867

39-
# Funding Sources
68+
.hero-section p {
69+
font-size: 1.25rem;
70+
color: var(--text-secondary);
71+
max-width: 800px;
72+
margin: 0 auto;
73+
}
74+
75+
/* Content section */
76+
.content-section {
77+
max-width: 800px;
78+
margin: 0 auto;
79+
padding: 2rem 1rem;
80+
}
81+
82+
.content-section h2 {
83+
font-size: 2rem;
84+
font-weight: 700;
85+
color: var(--primary-color);
86+
margin-bottom: 1.5rem;
87+
position: relative;
88+
}
89+
90+
.content-section h2::after {
91+
content: '';
92+
position: absolute;
93+
bottom: -10px;
94+
left: 0;
95+
width: 60px;
96+
height: 4px;
97+
background: linear-gradient(90deg, var(--secondary-color), var(--accent-color));
98+
border-radius: 2px;
99+
}
100+
101+
.content-section p {
102+
font-size: 1.1rem;
103+
color: var(--text-secondary);
104+
line-height: 1.6;
105+
margin-bottom: 1.5rem;
106+
}
107+
108+
.content-section a {
109+
color: var(--secondary-color);
110+
text-decoration: none;
111+
transition: var(--transition);
112+
}
113+
114+
.content-section a:hover {
115+
color: var(--accent-color);
116+
text-decoration: underline;
117+
}
118+
119+
/* Funding section */
120+
.funding-section {
121+
text-align: center;
122+
padding: 4rem 1rem;
123+
margin: 0 auto 3rem;
124+
max-width: 800px;
125+
background-color: var(--card-bg);
126+
border-radius: var(--radius);
127+
box-shadow: var(--shadow);
128+
}
129+
130+
.funding-section h2 {
131+
font-size: 2rem;
132+
font-weight: 700;
133+
color: var(--primary-color);
134+
margin-bottom: 1.5rem;
135+
position: relative;
136+
}
137+
138+
.funding-section h2::after {
139+
content: '';
140+
position: absolute;
141+
bottom: -10px;
142+
left: 50%;
143+
transform: translateX(-50%);
144+
width: 60px;
145+
height: 4px;
146+
background: linear-gradient(90deg, var(--secondary-color), var(--accent-color));
147+
border-radius: 2px;
148+
}
149+
150+
.funding-section img {
151+
max-width: 100%;
152+
height: auto;
153+
margin-top: 1.5rem;
154+
}
155+
156+
/* Responsive adjustments */
157+
@media (max-width: 768px) {
158+
.hero-section h1 {
159+
font-size: 2rem;
160+
}
161+
162+
.content-section, .funding-section {
163+
padding: 2rem 1rem;
164+
}
165+
}
166+
</style>
167+
168+
::: {.hero-section}
169+
![](../contents/logo/bioconductor_logo_cmyk.svg)
170+
171+
# Bioconductor: Open Source Software for Genomics
172+
173+
Providing Bioconductor training by redeveloping the website and developing global infrastructure to deliver high-quality community-led training in local languages.
174+
:::
175+
176+
::: {.content-section}
177+
## About Bioconductor
178+
179+
[Bioconductor](https://www.bioconductor.org) is an open-source, open-development software project in the R statistical software language and is widely used in bioinformatics, immunology, microbiology, and single-cell genomics. Over 1,200 developers have contributed software that is downloaded by users over 500,000 times per year.
180+
181+
In April 2020, we established a **Community Advisory Board (CAB)** that includes elected representatives from America, Europe, Africa, Asia, and Latin America to outreach to the growing global Bioconductor community. The CAB identified accessible high-quality training materials and delivery methods as an urgent, impactful need. Fundamental components for a successful training platform include:
182+
183+
- Skilled and effective program management.
184+
- Excellence in instruction.
185+
- Quality of training materials.
186+
- Equity in access.
187+
188+
This proposal will redevelop the Bioconductor web presence to ensure Bioconductor communities have equitable access to quality, well-structured project information and training materials. This work will also deliver structured, high-quality, culturally-aware, inclusive global training by developing a platform for community-led instruction.
189+
190+
## Publications
191+
192+
- [@Reimers2006]
193+
194+
## Collaborations
195+
196+
Our lab supports the open-source bioinformatics community and is working with:
197+
198+
- [ELIXIR](https://elixir-europe.org): European Infrastructure for life-science information.
199+
- [LERO](https://lero.ie): Ireland's open-source software research center.
200+
201+
![ELIXIR Logo](../contents/logo/Elixir_logo-3927606181.png){width="147"} ![LERO Logo](../contents/logo/lero.png){width="202"}
202+
:::
203+
204+
::: {.funding-section}
205+
## Funding Sources
40206

41207
This project is funded by a [Chan Zuckerberg Initiative](https://chanzuckerberg.com/eoss/proposals/bioconductor-high-quality-training-and-support-for-a-worldwide-community/) CZI Science Essential Open Source Software (EOSS) award to Aedin Culhane.
42208

43209
![](../contents/logo/CZI_science.png){width="334"}
210+
:::

0 commit comments

Comments
 (0)