Skip to content

Commit 808e7ac

Browse files
adamjohnwrightadamjohnwright
authored
Updateing GSOC pages for 2026 (#74)
* Update GSoC references from 2024 to 2026 Also updated numbers for gsoc stats * Update document for GSOC Project Ideas to 2026 * Update mentor information and project details * Change contact emails for GSoC inquiries Updated contact information for students and mentors. * Simplify contact information for students and mentors Removed email links for Robin and Adam, simplifying the text. * Revise submission instructions and clean up content Updated instructions for submitting project ideas and removed unnecessary content.
1 parent 4e9cbe0 commit 808e7ac

2 files changed

Lines changed: 227 additions & 21 deletions

File tree

‎wiki/GSOC_Project_Ideas_2026.md‎

Lines changed: 205 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,205 @@
1+
2+
3+
4+
<span id="top"></span>
5+
6+
7+
8+
9+
# <span dir="auto">GSOC Project Ideas 2026</span>
10+
11+
12+
13+
14+
15+
16+
17+
18+
19+
*Got an idea for [GSOC 2026](GSoC "GSoC")?'*
20+
21+
Then please post it. You can either
22+
23+
1. Add it here, by directly editing this page. Just copy, paste and
24+
update the [template](#Template) below. This requires that you create
25+
a fork of this repo and then make a pull request with the changes.
26+
27+
Projects can use a broad set of skills, technologies, and domains, such
28+
as GUIs, database integration and algorithms.
29+
30+
Students are also encouraged to propose their own ideas related to our
31+
projects. If you have strong computer skills and have an interest in
32+
biology or bioinformatics, you should definitely apply! Do not hesitate
33+
to propose your own project idea: some of the best applications we see
34+
are by students who go this route. As long as it is relevant to one of
35+
our projects, we will give it serious consideration. Creativity and
36+
self-motivation are great traits for open-source programmers.
37+
38+
39+
40+
# <span id="Proposed_project_ideas_for_2026" class="mw-headline">Proposed project ideas for 2026</span>
41+
42+
## <span id="MP-BioPath_Perturation_Analysis_.2F_Stein_Lab" class="mw-headline">MP-BioPath Perturation Analysis / Stein Lab</span>
43+
44+
- *Brief explanation:* MP-BioPath is a computational tool designed to
45+
predict the effects of perturbations on biological pathways. Utilizing
46+
Reactome's pathway models, MP-BioPath employs an optimization model.
47+
Our objective is to develop pipelines and tools that integrate
48+
MP-BioPath results with genomic data.
49+
- *Expected results:* As a result of this project, we aim to develop
50+
tools and pipelines capable of handling diverse genomic datasets.
51+
Additionally, we anticipate the generation of novel biologically
52+
significant insights.
53+
- *Project Home Page URL:*
54+
<a href="https://reactome.org" class="external text"
55+
rel="nofollow">Reactome</a>
56+
<a href="https://github.com/OICR/mp-biopath" class="external text"
57+
rel="nofollow">MP-BioPath</a>
58+
- *Project paper reference and URL:*
59+
<a href="https://doi.org/10.1093%2Fdatabase%2Fbaac009"
60+
class="external text" rel="nofollow">"Evaluating the predictive accuracy
61+
of curated biological pathways in a public knowledgebase"</a>
62+
- *Knowledge prerequisites:* Python, R, Julia
63+
- *Skill level:* Medium
64+
- *Project Time:* 175-hour approximately 8 weeks
65+
- *Mentors:* Adam Wright \<adam.wright@oicr.on.ca\>
66+
67+
## <span id="Pathway_Reasoning_with_LLM_.2F_Stein_Lab" class="mw-headline">Pathway Reasoning with LLM / Stein Lab</span>
68+
69+
- *Brief explanation:* Reactome houses a meticulously curated repository
70+
of human biological pathways. Our current initiative focuses on
71+
crafting a RAG chat application optimized for intuitive interaction
72+
with the Reactome web portal. Our primary aim is to empower the
73+
application to interpret user queries and leverage the LLM (Language
74+
Model) to delve deep into pathway structures, enabling the generation
75+
of comprehensive and insightful responses for users.
76+
- *Expected results:* expected outcomes include the application's
77+
ability to effectively handle a diverse range of user queries and to
78+
expand its capabilities to accommodate an increased number of use
79+
cases. Furthermore, the application is expected to leverage advanced
80+
reasoning capabilities powered by the LLM, thereby providing more
81+
insightful and comprehensive responses tailored to each user's inquiry
82+
- *Project Home Page URL:*
83+
<a href="https://reactome.org" class="external text"
84+
rel="nofollow">Reactome</a>
85+
- *Project paper reference and URL:*
86+
- *Knowledge prerequisites:* Python, RAG
87+
- *Skill level:* Medium
88+
- *Project Time:* 175-hour approximately 8 weeks
89+
- *Mentors:* Adam Wright \<adam.wright@oicr.on.ca\>
90+
91+
92+
## <span id="Reactome-MCP_.2F_Stein_Lab" class="mw-headline">Reactome MCP / Stein Lab</span>
93+
94+
- *Brief explanation:* Reactome provides users with various computational
95+
interfaces for computationally accessing the curated biological pathways,
96+
including analysis tools and a chat interface React-to-Me. A Reactome MCP would
97+
make the website more computationally accessible by providing access to the tools
98+
through React-to-Me and other LLM based chat interfaces.
99+
- *Expected results:* expected outcomes include the application's
100+
ability to run Reactome analysis tools through the React-to-Me chat interface.
101+
Other features of Reactome, including our REST APIs, should be made accessible
102+
to LLMs through the MCP.
103+
- *Project Home Page URL:*
104+
<a href="https://reactome.org/chat" class="external text"
105+
rel="nofollow">React-to-Me</a>
106+
- *Project paper reference and URL:*
107+
- *Knowledge prerequisites:* Python, RAG, MCP
108+
- *Skill level:* Medium
109+
- *Project Time:* 175-hour approximately 8 weeks
110+
- *Mentors:* Adam Wright \<adam.wright@oicr.on.ca\>
111+
112+
# <span id="Project_template" class="mw-headline">Project template</span>
113+
114+
## <span id="Template:_Project_Idea_Name_.28Project_Name.2FLab_Name.29" class="mw-headline">Template: Project Idea Name (Project Name/Lab Name)</span>
115+
116+
- *Brief explanation:* Brief description of the idea, including any
117+
relevant links, etc.
118+
- *Expected results:* describe the outcome of the project idea.
119+
- *Project Home Page URL:* if there is one.
120+
- *Project paper reference and URL:* Is there a paper about the project
121+
this effort will be a part of?
122+
- *Knowledge prerequisites:* programming language(s) to be used, plus
123+
any other particular computer science skills needed.
124+
- *Skill level:* Basic, Medium or Advanced.
125+
- *Project Time:* 90-hour, 90, 175 or 350 hours that are a standard 8
126+
weeks long and no longer than 12 weeks.
127+
- *Mentors:* name + contact details of the lead mentor, name + contact
128+
details of 1 or 2 backup mentors.
129+
130+
131+
132+
133+
134+
135+
136+
137+
## Navigation menu
138+
139+
140+
141+
142+
143+
144+
145+
146+
147+
### Navigation
148+
149+
150+
151+
- <span id="n-GMOD-Home">[GMOD Home](Main_Page)</span>
152+
- <span id="n-Software">[Software](GMOD_Components)</span>
153+
- <span id="n-Categories-.2F-Tags">[Categories /
154+
Tags](Categories)</span>
155+
156+
157+
158+
159+
### Documentation
160+
161+
162+
163+
- <span id="n-Overview">[Overview](Overview)</span>
164+
- <span id="n-FAQs">[FAQs](Category%253AFAQ)</span>
165+
- <span id="n-HOWTOs">[HOWTOs](Category%253AHOWTO)</span>
166+
- <span id="n-Glossary">[Glossary](Glossary)</span>
167+
168+
169+
170+
171+
### Community
172+
173+
174+
175+
- <span id="n-GMOD-News">[GMOD News](GMOD_News)</span>
176+
- <span id="n-Training-.2F-Outreach">[Training /
177+
Outreach](Training_and_Outreach)</span>
178+
- <span id="n-Support">[Support](Support)</span>
179+
- <span id="n-GMOD-Promotion">[GMOD Promotion](GMOD_Promotion)</span>
180+
- <span id="n-Meetings">[Meetings](Meetings)</span>
181+
- <span id="n-Calendar">[Calendar](Calendar)</span>
182+
183+
184+
185+
186+
### Tools
187+
188+
- <span id="t-smwbrowselink"><a href="Special%253ABrowse/GSOC_Project_Ideas_2026" rel="smw-browse">Browse
189+
properties</a></span>
190+
191+
192+
193+
- <span id="footer-info-lastmod">Last updated at 16:41 on 12 February
194+
2026.</span>
195+
<!-- - <span id="footer-info-viewcount">850 page views.</span> -->
196+
- <span id="footer-info-copyright">Content is available under
197+
<a href="http://www.gnu.org/licenses/fdl-1.3.html" class="external"
198+
rel="nofollow">a GNU Free Documentation License</a> unless otherwise
199+
noted.</span>
200+
201+
<!-- -->
202+
203+
204+
205+
<!-- -->

‎wiki/GSoC.md‎

Lines changed: 22 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -30,15 +30,15 @@ width="373" height="373" alt="GoogleSummer 2016logo.jpg" />](GSoC "GSoC")
3030

3131

3232
- [<span class="tocnumber">1</span> <span class="toctext">Google Summer
33-
of Code 2024 @ Open Genome
34-
Informatics</span>](#Google_Summer_of_Code_2024_.40_Open_Genome_Informatics)
33+
of Code 2026 @ Open Genome
34+
Informatics</span>](#Google_Summer_of_Code_2026_.40_Open_Genome_Informatics)
3535
- [<span class="tocnumber">2</span> <span class="toctext">Mailing lists,
3636
IRC, and other ways to get in
3737
touch</span>](#Mailing_lists.2C_IRC.2C_and_other_ways_to_get_in_touch)
3838
- [<span class="tocnumber">3</span> <span class="toctext">Project
3939
Ideas</span>](#Project_Ideas)
4040
- [<span class="tocnumber">4</span> <span class="toctext">Preparing for
41-
GSoC 2024</span>](#Preparing_for_GSoC_2024)
41+
GSoC 2026</span>](#Preparing_for_GSoC_2026)
4242
- [<span class="tocnumber">4.1</span>
4343
<span class="toctext">Contributors</span>](#Contributors)
4444
- [<span class="tocnumber">4.2</span>
@@ -48,25 +48,25 @@ width="373" height="373" alt="GoogleSummer 2016logo.jpg" />](GSoC "GSoC")
4848

4949

5050

51-
## <span id="Google_Summer_of_Code_2024_.40_Open_Genome_Informatics" class="mw-headline">Google Summer of Code 2024 @ Open Genome Informatics</span>
51+
## <span id="Google_Summer_of_Code_2026_.40_Open_Genome_Informatics" class="mw-headline">Google Summer of Code 2026 @ Open Genome Informatics</span>
5252

5353
**<a href="https://summerofcode.withgoogle.com/" class="external text"
5454
rel="nofollow">Google Summer of Code</a>** is a global program that
5555
offers students, developers, and other contributors stipends to write
5656
code for various open-source software projects. We work with many
5757
open-source, free software, and technology-related groups to identify
58-
and fund projects over a 12+ week period. Since its inception seventeen
59-
years ago, the program has brought together over 20,000 successful
60-
participants from 116 countries, 850+ open-source organizations, and has
61-
generated over 45 million lines of code. Through Google Summer of Code,
58+
and fund projects over a 12+ week period. Since its inception, twenty-one
59+
years ago, the program brought together over 22,000 successful
60+
participants from 123 countries, 1200+ open-source organizations, and has
61+
generated over 48 million lines of code. Through Google Summer of Code,
6262
accepted applicants are paired with a mentor or mentors from the
6363
participating projects, thus gaining exposure to real-world software
6464
development scenarios and the opportunity for employment in areas
6565
related to their academic pursuits. In turn, the participating projects
66-
are able to more easily identify and bring in new developers. Best of
66+
can more easily identify and bring in new developers. Best of
6767
all, more source code is created and released for the use and benefit of
6868
all. The program is open to students and to beginners in open source
69-
software development. The length of the projects is 90, 175 and
69+
software development. The length of the projects is 90, 175, and
7070
350-hours, and there is an option to extend the program from the
7171
standard 12 weeks up to 22 weeks. (*Excerpt from the
7272
<a href="https://summerofcode.withgoogle.com/" class="external text"
@@ -98,7 +98,9 @@ class="external text" rel="nofollow">FAQ</a>.
9898

9999
## <span id="Mailing_lists.2C_IRC.2C_and_other_ways_to_get_in_touch" class="mw-headline">Mailing lists, IRC, and other ways to get in touch</span>
100100

101-
- Email: <a href="mailto:rhaw@oicr.on.ca" class="external text"
101+
- Email: <a href="mailto:awright@oicr.on.ca" class="external text"
102+
rel="nofollow">awright@oicr.on.ca</a>,
103+
<a href="mailto:rhaw@oicr.on.ca" class="external text"
102104
rel="nofollow">rhaw@oicr.on.ca</a> **and**
103105
<a href="mailto:help@gmod.org" class="external text"
104106
rel="nofollow">help@gmod.org</a> -- find out more about GSoC, a
@@ -108,14 +110,13 @@ class="external text" rel="nofollow">FAQ</a>.
108110
class="external text" rel="nofollow">Genome Informatics Google
109111
Groups</a> - ask about our projects; join the community!
110112
- Students and Mentors can email both
111-
[Robin](User%253ARobin.haw "User%253ARobin.haw") and
112-
[Scott](User%253AScott "User%253AScott") to get more information about the
113+
Robin and Adam to get more information about the
113114
program.
114115

115-
## <span id="Project_Ideas" class="mw-headline"> [Project Ideas](GSOC_Project_Ideas_2024 "GSOC Project Ideas 2024")</span>
116+
## <span id="Project_Ideas" class="mw-headline"> [Project Ideas](GSOC_Project_Ideas_2026 "GSOC Project Ideas 2026")</span>
116117

117118
**Got an idea for a GSOC project? [Add it
118-
here](GSOC_Project_Ideas_2022 "GSOC Project Ideas 2022").** Ideas will
119+
here](GSOC_Project_Ideas_2026 "GSOC Project Ideas 2026").** Ideas will
119120
be included in the proposal we send to GSOC, and great ideas make for a
120121
great proposal, so please add yours now.
121122

@@ -125,15 +126,15 @@ encouraged to propose their own ideas related to our projects. If you
125126
have strong computer skills and have an interest in biology or
126127
bioinformatics, you should definitely apply!
127128
**Do not hesitate to propose your own project idea: some of the best
128-
applications we see are by students that go this route.** As long as it
129+
applications we see are by students who go this route.** As long as it
129130
is relevant to one of our projects, we will give it serious
130131
consideration. Creativity and self-motivation are great traits for
131132
open-source programmers.
132133

133-
## <span id="Preparing_for_GSoC_2024" class="mw-headline">Preparing for GSoC 2024</span>
134+
## <span id="Preparing_for_GSoC_2026" class="mw-headline">Preparing for GSoC 2026</span>
134135

135-
Right now it is the organization application process for GSoC - we won't
136-
know if Open Genome Informatics has been accepted as a GSOC 2024
136+
Right now, it is the organization application process for GSoC - we won't
137+
know if Open Genome Informatics has been accepted as a GSOC 2026
137138
mentoring organization until
138139
<a href="https://developers.google.com/open-source/gsoc/timeline"
139140
class="external text" rel="nofollow">February 22nd</a>. Nevertheless, it
@@ -151,7 +152,7 @@ available closer to the start of the student application period.
151152

152153
We encourage mentors and mentoring organizations to think about new
153154
projects year-round! If you'd like help with your ideas page or your
154-
separate mentoring org application, please feel to contact the
155+
separate mentoring org application, please feel free to contact the
155156
organization admins. Links to [advice about mentoring and other
156157
resources](GSOC_Mentoring_Guide "GSOC Mentoring Guide") are available.
157158

@@ -235,7 +236,7 @@ repositories](Source_Code_Repositories "Source Code Repositories").
235236

236237

237238
- <span id="footer-info-lastmod">Last updated at 16:07 on 12 February
238-
2024.</span>
239+
2026.</span>
239240
<!-- - <span id="footer-info-viewcount">809,743 page views.</span> -->
240241
- <span id="footer-info-copyright">Content is available under
241242
<a href="http://www.gnu.org/licenses/fdl-1.3.html" class="external"

0 commit comments

Comments
 (0)