Graduate Research Assistant
The Tulane University Biodiversity Research Institute (TUBRI) is a research center of Tulane's School of Science and Engineering, located on the grounds of the F. Edward Hebert Research Center in Belle Chasse, Louisiana, a suburb of New Orleans. TUBRI houses the Royal D. Suttkus Fish Collection and specializes in biodiversity discovery (primarily fishes) and biodiversity informatics research. Henry L. Bart, Jr., Professor of Ecology and Evolutionary Biology serves as TUBRI Director and Yasin Bakış is Senior Manager of Biodiversity Informatics and Data Engineering for the center.
A Graduate Research Assistant is sought to support the research of the newly funded, NSF Harnessing the Data Revolution Institute project entitled, Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning. The project involves using Machine-Learning methods to train neural networks to extract phenotypic trait data from images of fish specimens, aided by a fish anatomy ontology and trees depicting phylogenetic relationships among tested fish species.
The successful candidate will actively participate in the research of the project under the mentorship of Bart and Bakış.
Desired Knowledge, Skills, and Abilities
Working knowledge of at least 2 of the following languages (one from each group)
{Java, C, C++, C#}, {Python, PHP, Perl}, {R, Bash, JavaScript}, {ORACLE SQL, MSSQL, PostgreSQL, MySQL}
Required Education and/or Experience
BSc in Biology, Computer Science, Information Sciences, or a related field
Should commit to complete PhD study in Ecology and Evolutionary Biology (EEB) or Interdisciplinary EEB and Computer Science
Preferred Qualifications
MSc in Biology, Computer Science, Information Sciences or a related field
Working knowledge of Unix based operating systems
Prior experience in one of the following fields; Image Processing, Artificial Intelligence, Genetic Algorithms, Biodiversity Informatics, Computational Biology, Bioinformatics, Biomedical Informatics, Ecoinformatics or a related field (publications)
experience in Image Processing projects
experience in Artificial Intelligence/Neural Networks projects
experience in web-database applications
experience in Genetic Algorithms
Other requirement for the position
Admission the Ph.D. program in Ecology and Evolutionary Biology at Tulane University
The position is open to international candidates
Should be able to travel internationally
Strong communication and interpersonal skills
The project is in progress, and the position is available as early as January 2022. However, we are willing to delay the start until Summer or Fall 2022 for a qualified and highly motived student.
For additional information, please contact Henry Bart (hbartjr(a)tulane.edu<mailto:hbartjr@tulane.edu>) and Yasin Bakiş (ybakis(a)tulane.edu<mailto:ybakis@tulane.edu>).
Register for an account here: https://sse.tulane.edu/academics/graduate/admissions
Henry L. Bart Jr., Ph.D.
Director, Tulane University Biodiversity Research Institute
Curator, Royal D. Suttkus Fish Collection
3705 Main Street, Belle Chasse, LA 70037
Voice: 504-394-1711; Fax: 504-394-5045
Professor of Ecology and Evolutionary Biology, Tulane University
400 Lindy Boggs Hall, New Orleans, LA 70118
Voice: 504-862-8283; Fax 504-862-8706
Website: http://people.tubri.org/hank/
Postdoctoral Research Associate
The Tulane University Biodiversity Research Institute (TUBRI) is a research center of Tulane's School of Science and Engineering, located on the grounds of the F. Edward Hebert Research Center in Belle Chasse, Louisiana, a suburb of New Orleans. TUBRI houses the Royal D. Suttkus Fish Collection and specializes in biodiversity discovery (primarily fishes) and biodiversity informatics research. Henry L. Bart, Jr., Professor of Ecology and Evolutionary Biology serves as TUBRI Director and Yasin Bakış is Senior Manager of Biodiversity Informatics and Data Engineering for the center.
A postdoctoral research associate is sought to provide biological expertise and insight to the newly funded, NSF Harnessing the Data Revolution Institute project entitled, Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning. The project involves using Machine-Learning methods to train neural networks to extract phenotypic trait data from images of fish specimens, aided by a fish anatomy ontology and trees depicting phylogenetic relationships among tested fish species.
The successful candidate will actively participate in the research of the project under the mentorship of Bart and Bakış.
1. Analyzing images of fish specimens and corresponding metadata and creating reports based on the statistics about the data
2. Extracting morphological traits from fish specimen images to verify species identity
3. Designing and following workflows and pipelines for processing images and using extracted morphological traits data in "morphological barcoding" experiments for diagnosing the various taxonomic groups.
4. Verifying project outputs for scientifically accuracy
5. Support the coding team by
* assisting in software design where biological expertise is needed
* making sure the software is properly documented and openly accessible
* providing scientific input during the coding process so that outputs are scientifically sound and publishable
6. Attending related workshops, training programs, and meetings
7. Keeping abreast of the latest literature and openly sharing finding with project collaborators,
8. Work collaboratively with Imageomics ML experts to explore deep-learning methods,
9. Perform scientific analyses based on outputs of the project
10. Present analysis results at conferences and publish findings at scientific journals.
Required Knowledge, Skills, and Abilities
Prior (proven) experience in at least one of the following fields:
Image Processing, Artificial Intelligence, Genetic Algorithms, Biodiversity Informatics, Computational Biology, Bioinformatics, Biomedical Informatics, Ecoinformatics or a related field (scientific publications)
Working knowledge of at least three of the following languages (one from each group)
{Java, C, C++, C#}, {Python, PHP, Perl}, {R, Bash, JavaScript}, {ORACLE SQL, MSSQL, PostgreSQL, MySQL}
Working knowledge of Unix based operating systems
Experience in writing grant proposals and scientific publications
Strong problem-solving skills
Required Education and/or Experience
PhD in Biological Sciences, Biodiversity Informatics, Computer Science, Information Sciences, Computational Biology/Bioinformatics, or a related field
Preferred Qualifications
Experience with:
Image Processing
Artificial Intelligence/Neural Networks
Genetic Algorithms
Web-database applications
Experience in parallel computing (GPU)
Working knowledge of version control system (GIT)
Other
Position is open to international candidates
Should be able to travel internationally
Strong communication and interpersonal skills
Start date: 1 February 2022
For additional information about the position, please contact Henry Bart (hbartjr(a)tulane.edu<mailto:hbartjr@tulane.edu>) or Yasin Bakiş (ybakis(a)tulane.edu<mailto:ybakis@tulane.edu>)
Apply here: https://apply.interfolio.com/99039
Please post to the TDWG List:
Computer Programmer
The Tulane University Biodiversity Research Institute (TUBRI) is a research center of Tulane's School of Science and Engineering, located on the grounds of the F. Edward Hebert Research Center in Belle Chasse, Louisiana, a suburb of New Orleans. TUBRI houses the Royal D. Suttkus Fish Collection and specializes in biodiversity discovery (primarily involving fishes) and biodiversity informatics research. Henry L. Bart, Jr., Professor of Ecology and Evolutionary Biology serves as TUBRI Director and Yasin Bakış is Senior Manager of Biodiversity Informatics and Data Engineering for the center.
A computer programmer is sought to build cyberinfrastructure for accessing, hosting and sharing images of fish specimens from institutional image repositories and iNaturalist for use by investigators in the newly-funded, NSF Harnessing the Data Revolution Institute project entitled, Imageomics: A New Frontier of Biological Information Powered by Knowledge-Guided Machine Learning. The images will be used in Machine-Learning based, taxonomic identification and morphological trait extraction experiments, aided by a fish anatomy ontology and trees depicting phylogenetic relationships among tested fish species.
The successful candidate will perform the following tasks in the Imageomics Institute Project under the supervision of Bart and Bakış.
1. Create automation to process 700,000+ 2D images and associated metadata
2. Extract morphological traits including segmentation, shape outlines of specimens, strings of pixels representing color/pigment patterns from different areas of the fish image, color palette data, histogram data etc. to verify species identity
3. Build software for
a. Extracting several different types of morphological features from fish images automatically
b. Calculating the subsets of features (morphological barcodes) useful for identifying clusterings of images based on Genetic Algorithms Feature Selection methods
c. Implementing a Neural Network design for training computers in fish classification using the extracted morphological traits
d. Work collaboratively with other Imageomics Institute ML experts to explore deep-learning methods to capture species identification and trait data from other types of animal images.
Required Knowledge, Skills, and Abilities
1. Image Processing
2. Artificial Intelligence/Neural Networks
3. Genetic Algorithms
4. Working knowledge of following languages (one from each group)
Java, C, C++, C#}, {Python, PHP, Perl}, {R, Bash, JavaScript}, {ORACLE SQL, MSSQL, PostgreSQL, MySQL}
1. Unix based server management
2. Parallel programming (GPU)
3. Working knowledge of version control system (GIT)
4. Documenting the code
5. Ability to write clear, maintainable, portable code that conforms to standards and practices
6. Cross-platform experience
Required Education and/or Experience
College degree (Associates or Bachelors) in Computer Science, Information Sciences, Biology, and related fields. Must have at least 3 years of programming experience
Preferred Qualifications
MSc or PhD in computational biology, bioinformatics, biology or a related field
Experience in web-database applications
Prior experience with Biological datasets
Other Requirements
The position is open to international candidates
Candidate should be able to travel internationally
Start date: The position is open for immediate hire. Preferred starting date is 4 February 2022
For additional information about the position, please contact Henry Bart (hbartjr(a)tulane.edu<mailto:hbartjr@tulane.edu>) or Yasin Bakiş (ybakis(a)tulane.edu<mailto:ybakis@tulane.edu>)
Apply here: https://jobs.tulane.edu/position/IRC22108
Thank you!
Henry L. Bart Jr., Ph.D.
Director, Tulane University Biodiversity Research Institute
Curator, Royal D. Suttkus Fish Collection
3705 Main Street, Belle Chasse, LA 70037
Voice: 504-394-1711; Fax: 504-394-5045
Professor of Ecology and Evolutionary Biology, Tulane University
400 Lindy Boggs Hall, New Orleans, LA 70118
Voice: 504-862-8283; Fax 504-862-8706
Website: http://people.tubri.org/hank/
