Volunteership 2025: Difference between revisions

From HIVE Lab
Jump to navigation Jump to search
← Older editNewer edit →
VisualWikitext
Add biomarker curation project ideas
mNo edit summary
Line 19: Line 19:
<ol>
<ol>
   <li>BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.</li>
   <li>BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.</li>
   <li>GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information. </li><li>ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies. </li><li>PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models </li></ol>Individuals with a background in programming and/or machine learning may take on additional tasks that contribute to the development of ML models, which can be integrated into PredictMod (<nowiki>https://hivelab.biochemistry.gwu.edu/predictmod</nowiki>).
   <li>GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information. </li><li>ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies. </li><li>PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models. </li></ol>Individuals with a background in programming and/or machine learning may take on additional tasks that contribute to the development of ML models, which can be integrated into PredictMod (<nowiki>https://hivelab.biochemistry.gwu.edu/predictmod</nowiki>).
<hr>
<hr>


Revision as of 20:16, 3 April 2025

<html>

2025 Volunteer Program Details

Dates

June 2nd, 2025 – July 25th, 2025 (8 weeks)
Monday to Friday | Remote | No breaks

Volunteer Expectations

  1. Daily progress updates via Slack (scrum).
  2. Regular Zoom meetings with the assigned project point of contact.
  3. Expected to dedicate 5–6 hours per day to project work, with the remaining time focused on skill development or reading.

Important: If the scrum is not updated for 2 consecutive days, the candidate will be automatically dropped from the program.

Potential Projects

  1. BiomarkerKB (biomarkerkb.org) project: Biomarker curation project. Involves reading papers and collecting biomarkers.
  2. GlyGen (glygen.org) project: Review glycomics and glycoproteomics data and curate tissue, disease, and other related information.
  3. ARGOS (argosdb.org) project: Analyze genomics data using HIVE to identify reference genome assemblies.
  4. PredictMod (hivelab.biochemistry.gwu.edu/predictmod) project. Identifying datasets and harmonizing them so that they can be used to generate ML models.

Individuals with a background in programming and/or machine learning may take on additional tasks that contribute to the development of ML models, which can be integrated into PredictMod (https://hivelab.biochemistry.gwu.edu/predictmod).

BiomarkerKB Biocuration Project Ideas

  1. Curate biomarkers for a specific disease (Alzheimers)
    1. Student would work on doing manual curation for about 4 weeks, with regular check-ins with me to ensure it is being done correctly
    2. Next 4 weeks can work on developing an LLM or automated process to extract biomarker details with data collected in the first 4 weeks as training data/example data
  2. Top 50 biomarkers
    1. curate the top 50 biomarkers for biomarkerkb.org
    2. Define what constitutes a top 50 biomarker
    3. Begin curating biomarkers from different sources and papers by collecting fields mentioned in data model and collecting cross-references as well.
  3. Biocuration of biomarkers from NLP/LLM work
    1. Use the biomarkers collected from NLP work
    2. Curate biomarkers. Data provided was not provided in biomarker data model
    3. While curating biomarkers also check if data collected from NLP is correct
    4. After completion student can start using curated data to work on NLP/LLM method
  4. Curate biomarkers for a treatment
    1. same as number 1 above

If the student has any other ideas, diseases, treatments, or methods they want to focus on please reach out to daniallmasood@gwu.edu to discuss your idea and check if it will be feasible as a project for the summer.

Requirements for Completion

Note: The following are mandatory. Failure to complete any will result in an incomplete volunteer record.

Documentation

All volunteers must maintain adequate documentation of their work, including written protocols and scripts submitted to GitHub.

Written Report

Submit a 1–2 page summary of your tasks and accomplishments to the Admin Team during the final week of your program.

Presentation & Slide Submission

Present your work last week of the 8-week period.

Slides must be submitted to the Admin Team and should include:

  • A title slide with your name, date, and mentor
  • At least 3 content slides
  • A final slide with acknowledgements or references

Contact the Admin Team to access previously submitted slides.

Completion Certificate

A certificate of completion and a letter of recommendation will be provided to all participants who successfully complete the program.

Contact

mazumder_lab AT gwu.edu.

Retrieved from "https://hivelab.biochemistry.gwu.edu/wiki/index.php?title=Volunteership_2025&oldid=648"