Job Opportunities

Angular Software Developer


Indiana University's Cyberinfrastructure for Network Science Center (CNS) is looking for part-time Angular software developers to become an integral member of a professional development team implementing advanced web applications.

Qualifications: At least 1 year of professional experience with Angular 10+ technology. Preference for experience in TypeScript, Angular, D3, or Vega. Experience with CSS and a compiler like SCSS. Experience in cross-disciplinary teams and strong collaboration skills.

Employment type: Part-time

Location: Bloomington, Indiana, United States. Work for this position must be performed in person at the CNS offices in Luddy Hall.

TO APPLY: Please email cnscntr@iu.edu. Please use “Angular Developer Position” as the subject line.

About the Cyberinfrastructure for Network Science Center (CNS): CNS is a research center at Indiana University’s Luddy School of Informatics, Computing, and Engineering in Bloomington, Indiana (http://cns.iu.edu). For 20 years, CNS has played a leading role in the field of data visualization, developing open source tools for the creation of data visualizations, co-organizing international workshops and conferences, and promoting network science and visualization through international initiatives. CNS’s research, teaching, and software development efforts benefit from long-term collaborations with colleagues in academia, government, and industry.



Hourly Research Assistant


The Cyberinfrastructure for Network Science (CNS) Center is seeking a part-time (up to 20 hours per week) Hourly Research Assistant for Cell Type Annotation (CTann) to support the work of a growing research center that focuses on data visualization. This individual will work under the direction of faculty and staff to implement and productize a computational pipeline to annotate cell-by-gene matrices using CTann tools such as Azimuth, CellTypist, popV, and the upcoming pan-organ Azimuth. Work needs to take place in person at the CNS office in Luddy Hall, IU Bloomington. The individual hired will work as part of our research team in collaboration with our development team, and they will report to the Research Lead.

These tasks involve a variety of coding tasks, potentially including but not limited to:
  • Understanding, running, and optimizing CTann tools and integrating them into the HRA Workflows Runner, see https://www.biorxiv.org/content/10.1101/2024.03.27.587041v3 for background
  • Attending stand-up meetings and reporting on progress
  • Contribute expertise and text to ongoing manuscripts 
  • Creating and managing GitHub issues
  • Creating pull requests
  • Presenting code to the CNS team or external collaborators

Qualifications: Advanced knowledge in Python and JavaScript (incl. best practices), basic knowledge of R, ability to read documentation for R packages, practical knowledge of npm package manager and node.js, and best practices for adding comments and collaborative code development using GitHub. Knowledge of Docker, Singularity, and advanced scripting is a plus.

How to apply:

Please submit a cover letter and resume to Nicole Johnson at ncj4@iu.edu by Feb 17, 2025. Please use “Hourly RA - CTann Position” as the subject line. Additionally, when applying, you are required to complete the CTann Assessment detailed below. Please include the GitHub link to your assessment solution in your application email. Applicants who have not submitted the assessment will not be considered. No extensions to solve the assessment will be given.

CTann Assessment:

Write a Jupyter Notebook that is well documented, easy to read, and can be re-run from scratch that performs the following tasks:

  1. Installs Python dependencies (at least anndata and requests, but you may need others)
  2. Downloads a cell-by-gene matrix (h5ad file) from HuBMAP. You may choose your own or use the expr.h5ad file provided on the HuBMAP Data Portal under this link.
  3. Runs the Azimuth cell type annotation tool over the matrix to determine cell types. This is an R program, so create an R script that can be executed from the Jupyter Notebook. See https://satijalab.github.io/azimuth/articles/run_azimuth_tutorial.html for a tutorial.
  4. Reads the annotated h5ad file into Python using the anndata library
  5. Computes the number of cells per cell type
  6. Visualizes the distribution of cells per cell type

After creating the notebook, publish the Jupyter Notebook to GitHub and document the steps taken, issues encountered, and results obtained in the README.md file for the repository.

The CNS mission is to advance research, development, teaching, and service in data mining, modeling, and visualization. Specific foci are increased data visualization literacy and research on multi-level atlases of the structure and evolution of science and technology (see Mapping Science Exhibit), mapping the human body at the single cell level (see HuBMAP, SenNet), and the communication of results via static and interactive data visualizations (see courses like the Visual Analytics Certificate and the Visible Human MOOC).



Biomedical Consultant


The biomedical consultant will work on the NIH-funded HuBMAP project, which aims to map the human body at single-cell level. They will join an interdisciplinary team that includes software developers, data scientists, medical illustrators, biologists, and project managers at CNS (https://cns.iu.edu). They will collaborate with external organ experts to catalogue and link anatomical structures, cell types, and biomarkers to the Human Reference Atlas (HRA), document work in standard operating procedures, and contribute to scientific publications. They will work with users of the HRA on defining and implementing existing and new use cases.

The ideal candidate will have strong oral and written communication skills and a unique combination of training and/or prior experience in more than one of the following areas: biomedical imaging, histology, human anatomy and physiology, data analysis, and single cell analyses. Familiarity with multiplexed microscopy image analysis software and molecular biology assays and bioinformatics is a plus. The biomedical expert will have an opportunity to co-author scholarly publications in high-profile scientific outlets.

This is a flexible, part-time position of up to 20 hours per week and could accommodate remote work for the right candidate, but would ideally be an in-person position on the Indiana University Bloomington campus. To apply, email cover letter and resume to Nicole Johnson at ncj4@iu.edu using “Biomedical Consultant position” as the subject line.

Responsibilities:
  • Supports efforts of leading scientists in harmonizing terminology across multiple areas of cellular biology.
  • Assists researchers in interpreting and using experimental data in HRA construction and usage.
  • Documents procedures in standard operating procedures (SOPs).
  • Attends relevant meetings, representing the project in a professional manner.
  • Collaborated on documenting results in scholarly publications.

Qualifications:
  • Education: Master’s degree in biology or a related field is strongly encouraged. Research experience in a higher education environment is preferred.
  • Experience: At least 2 years of experience working in a laboratory setting addressing biomolecular research questions. With a focus on single cell experimental designs and data analysis.
  • Required knowledge, skills, and abilities: Excellent written and oral communication skills. Problem solving skills. Must be willing to work in a team-oriented environment and must be a motivated self-starter.




Hourly Python Developer


The Cyberinfrastructure for Network Science (CNS) Center is seeking a part time (up to 20 hours per week) hourly research assistant to support the work of a growing research center that focuses on data visualization. This individual will work under the direction of staff as a Python developer, working on projects related to 3D image and point-cloud registration. Work needs to take place in person at the CNS office.

Qualifications: At least 1 year of professional experience with Python development. Experience with image registration, 3D imaging datasets, point cloud datasets, and Open3D is a must. Expertise with Blender to modify 3D assets is preferred. Experience in cross-disciplinary teams, strong collaboration and communication skills are a must. Applicants graduating in Spring/Summer 2025 need not apply.

Location: Work for this position must be performed in person at the CNS offices in Luddy Hall, at IU Bloomington.

The CNS mission is to advance research, development, teaching, and service in data mining, modeling, and visualization. Specific foci are increased data visualization literacy and research on multi-level atlases of the structure and evolution of science and technology (see Mapping Science Exhibit), mapping the human body at the single cell level (see HuBMAP, SenNet), and the communication of results via static and interactive data visualizations (see courses like the Visual Analytics Certificate and the Visible Human MOOC).

To apply, please submit a cover letter and resume to Nicole Johnson at ncj4@iu.edu by Feb 17, 2025. Please use “Hourly RA - AMAP Position” as the subject line. Additionally, when applying, you are required to complete a short assessment that is detailed below. Please make sure to include the GitHub link to your assessment solution in your email. Applicants who have not submitted the assessment will not be considered. No extensions to solve the assessment will be given.

AMAP Assessment:

As part of this position, you will primarily work with https://github.com/cns-iu/hra-amap. As part of the assessment, perform these tasks: