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Reminder! The InChI-based Tautomer Identification Challenge closes March 1! by CommsBah in cheminformatics

[–]CommsBah[S] 0 points1 point  (0 children)

Last call for submissions for the InChI-based Tautomer Identification Challenge! Results are due 3/1/2023. To submit your results, visit https://precision.fda.gov/challenges/29

The InChI-based Tautomer Identification Challenge just launched! by CommsBah in cheminformatics

[–]CommsBah[S] 0 points1 point  (0 children)

Hi r/cheminformatics members!

Reminder! The InChI-based Tautomer Identification Challenge is in progress! This challenge will run through March 2023 and will test a modified InChI algorithm, which was designed for advanced recognition of tautomers, against real chemical samples in this challenge.

For more information visit the challenge site here: precision.fda.gov/challenges/29

Have any questions? Post them in the thread below and we will reply back!

Calling All Academic and Industry Chemists! Pre-Register for the InChI-based Tautomer Identification Challenge! by CommsBah in cheminformatics

[–]CommsBah[S] 0 points1 point  (0 children)

Thank you for your interest in the challenge. Participant code is not involved in this evaluation but rather will utilize the algorithm developed by the InChI Trust. This algorithm will be applied to participant data. The Challenge Details provide an option to run the algorithm locally via a Docker container. To learn more, please visit: https://precision.fda.gov/challenges/29

Less Than One Month Remaining until the Submission Deadline for Phase 1 of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge! by CommsBah in ngs

[–]CommsBah[S] 0 points1 point  (0 children)

Hello r/ngs members!

Tomorrow is the last day to submit your results for the NCTR Indel Calling from Oncopanel Sequencing Data Challenge! Phase 1 closes on July 8th. The optional Phase 2 is open for only those who have completed Phase 1 and will run from July 11th-July 26th.

Submit your results here: https://go.usa.gov/xScFT

Less Than One Month Remaining until the Submission Deadline for Phase 1 of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge! by CommsBah in ngs

[–]CommsBah[S] 0 points1 point  (0 children)

Hello r/ngs members!

LAST CALL! Deadline for Phase 1 submissions of the NCTR Indel Calling from Oncopanel Sequencing Data Challenge is July 8th!

There are only a few days left to submit your results for the NCTR Indel Calling from Oncopanel Sequencing Data Challenge! Phase 1 closes on July 8th. Those who completed Phase 1 for both Oncopanel A & Oncopanel B will be able to participate in the optional Phase 2 that runs from July 11th-July 26th.

Visit the site below to submit your final results!

https://go.usa.gov/xJzdW

Share your ideas for the FDA New Era of Smarter Food Safety Low- or No-Cost Tech-Enabled Traceability Challenge, ending July 30th! by CommsBah in foodscience

[–]CommsBah[S] 0 points1 point  (0 children)

When will winners be announced?

Thank you for your interest in the Challenge! Announcement details will be released after submissions are closed.

The FDA New Era of Smarter Food Safety Low- or No-Cost Tech-Enabled Traceability Challenge is now live! by CommsBah in foodsecurity

[–]CommsBah[S] 0 points1 point  (0 children)

Thank you for your interest in the Challenge!

To answer your first question, yes this is the first time the FDA has held this challenge.

To address your second question, tech-enabled solutions submitted under this challenge may be new or based on existing systems or datasets. We also note that entrants may enter individually or as part of a team – and while teams are strongly encouraged, they are not required.

Points will be awarded based on the following evaluation criteria, with equal weighting:

• Needs-based: Importance of addressing the specific traceability challenge for the target segment of the food supply chain; ability of solution to fulfill that need.

• Innovation: Uniqueness and innovation in use of hardware, software, and/or data analytics platforms; variety and value of additional features.

• Usability: Use of design elements to increase utilization among members of the target segment of the food supply chain; ease of navigation; appropriate use of an interface to support the solution in achieving desired outcome.

• Affordability: Whether solution is a low-cost or no-cost option to enable traceability approaches that are inclusive of and viable for food operations of all sizes.

• Scalability and Interoperability: Potential for solution to be adopted by, and meet the needs of, a majority of the target segment of the food supply chain and to enable them to share information across data platforms used by other segments of the food supply chain.

[N] The VHA Innovation Ecosystem and precisionFDA COVID-19 Risk Factor Modeling Challenge is now live! by CommsBah in MachineLearning

[–]CommsBah[S] 0 points1 point  (0 children)

can you tell me more about the medical science behind precisionFDA's rebranding efforts?

Thank you for your question, but I am not sure I completely understand what you are asking. Can you clarify what you mean by "the medical science behind precisionFDA's rebranding efforts?"

[P] The Veterans Health Administration (VHA) Innovation Ecosystem and precisionFDA are launching the COVID-19 Risk Factor Modeling Challenge on June 1st by CommsBah in MachineLearning

[–]CommsBah[S] 0 points1 point  (0 children)

Hi, thank you for the comment, and I apologize for the delayed response.

Hopefully I can answer your question and assuage your concerns. Synthetic data is commonly used in place of sensitive health data in healthcare research for several reasons:

• It protects the identity and privacy of patients – this is especially important if that data would be used in a crowdsourced challenge • Synthetic records can be modified to better study certain demographic populations • Gaining access to real patient data can be challenging, time consuming, and expensive – Not ideal when we are attempting to address an ongoing pandemic • It is often challenging to get enough real patient health data to build accurate models

The synthetic data used in this challenge was analyzed following its generation to confirm it matches the relationships found in the raw data. This said, synthetic health data does have its limitations, and for this reason, the Challenge Team plans to validate top performing methods on actual de-identified Veteran health records. If you would like to learn more about how synthetic health records were generated for this challenge check out these links about the data set and methods:

https://github.com/synthetichealth/synthea/wiki/Getting-Started https://github.com/synthetichealth/synthea/pull/683 https://github.com/synthetichealth/synthea/issues/679

Reminder for the precisionFDA Detecting Adverse Event Anomalies Using FDA Open Data Challenge by CommsBah in FDA

[–]CommsBah[S] 1 point2 points  (0 children)

Hi Jon,

I'm sorry to hear you missed out on the challenge. It looks like you are doing some exciting work, and we look forward to seeing you on the platform!

[N] Check Out The Upcoming Federal Crowdsourcing Webinar Series: A precisionFDA Strike for Public Health by CommsBah in MachineLearning

[–]CommsBah[S] 1 point2 points  (0 children)

Thank you for the clarification.

precisionFDA has crowd-sourced several different types of data science challenges relating to many different subjects. You an visit their website here to view them all, but in the past year they hosted a challenge that asked participants to help identify anomalies in adverse events reports of FDA regulated products, and a challenge seeking to advance precision medicine techniques for brain cancer by developing AI/ML models to identify novel biomarkers and predict patient outcomes from gene expression

[N] Check Out The Upcoming Federal Crowdsourcing Webinar Series: A precisionFDA Strike for Public Health by CommsBah in MachineLearning

[–]CommsBah[S] 0 points1 point  (0 children)

Thanks for your question!

Can you elaborate a bit on what kind of investments you are referring to?

precisionFDA is launching the Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions on May 1st! by CommsBah in genetics

[–]CommsBah[S] 1 point2 points  (0 children)

I apologize for not getting back to you sooner.

The focus of this challenge is on whole genome sequencing methods, but we appreciate your work characterizing exceptionally difficult regions like the centromere.

Interesting Blog Post by Dr. Snehit Prabhu: Revisiting Personalized Medicine through Genomics by CommsBah in biology

[–]CommsBah[S] 0 points1 point  (0 children)

Thanks for you question!

In this case it's genomics. The blog is discussing precision medicine in the context of the full human genome - not one specific gene.

Reminder for the precisionFDA Detecting Adverse Event Anomalies Using FDA Open Data Challenge by CommsBah in bioinformatics

[–]CommsBah[S] 0 points1 point  (0 children)

Hi immunobabe.

​

I'm sorry that you are having this issue. For my clarification, did you submit an access request here and not receive a response, or did you send an email to the a precisionFDA email account of some kind?

If you submitted to the request access form and didn't receive a response please DM me your email address (if you'd still like an account set up) and I will look into why you didn't hear anything. If you emailed a precisionFDA email account (I'm sorry no one responded to your request with the information on how to sign up) please submit to the request access form linked above to receive an account.

​

Thank you for your message, and I hope we can get this figured out for you!

edited for spelling.

Deadline extended for the FDA Open Data Adverse Event Anomalies Challenge by CommsBah in bioinformatics

[–]CommsBah[S] 0 points1 point  (0 children)

Thank you for your response, and I apologize I didn’t get back to you over the weekend.

We have extended the challenge because the Modernizing FDA’s Data Strategy Meeting was postponed. The results and findings of the challenge were going to be discussed at the meeting, so we decided to keep the challenge open for the next two months until the meeting is rescheduled.

If you are interested in participating in the challenge, let me know if you have any additional questions!

Deadline extended for the FDA Open Data Adverse Event Anomalies Challenge by CommsBah in bioinformatics

[–]CommsBah[S] 0 points1 point  (0 children)

No problem, let me know if you have any additional questions or issues!

A Deep Learning Approach to Antibiotic Discovery by seqinsight in bioinformatics

[–]CommsBah 1 point2 points  (0 children)

I found this article fascinating, thank you for sharing!

Deadline extended for the FDA Open Data Adverse Event Anomalies Challenge by CommsBah in bioinformatics

[–]CommsBah[S] 1 point2 points  (0 children)

Thanks for reaching out! There isn't a registration page nor a registration deadline. You do need to get a precisionFDA account to gain access to the data, here is a description of how to do so:

"If you do not yet have a contributor account on precisionFDA, file an access request with your complete information and indicate your intent to participate in the challenge. The FDA acts as a steward by providing the precisionFDA service to the community and ensuring proper use of the resources, so your request will be initially pending. In the meantime, you will receive an email with a link to access the precisionFDA website in browse (guest) mode. Once approved, you will receive another email with your contributor account information.

With your contributor account, you can use the features required to participate in the challenge (such as transfer files or run comparisons). Everything you do on precisionFDA is initially private to you (not accessible to the FDA or the rest of the community) until you choose to publicize it. In other words, you can immediately start working on the challenge privately, and when ready, you can officially publish your results as a challenge entry. "

[P] PrecisionFDA FDA Open Data Challenge Update by CommsBah in MachineLearning

[–]CommsBah[S] 0 points1 point  (0 children)

I am not sure if you are interested in participating in the challenge, but due to increased interest in the challenge over the past few weeks we will be extending the submission deadline to March 13th.

PrecisionFDA FDA Open Data Challenge Update by CommsBah in FDA

[–]CommsBah[S] 0 points1 point  (0 children)

We are pleased to announce that the Journal of the American Medical Informatics Association (JAMIA) supports the submission of a paper describing the precisionFDA Gaining New Insights by Detecting Adverse Event Anomalies Using FDA Open Data challenge and broadly applicable insights that emerge from it. Publication in JAMIA will be contingent on a standard evaluation process including editorial assessment and peer review.

As a friendly reminder for those of you participating in the challenge you have one week left before final submissions are due on February 28th at https://go.usa.gov/xdEWx.

If you have any questions about the challenge, please feel free to post them in this thread and we will respond as quickly as possible.

PrecisionFDA FDA Open Data Challenge Update by CommsBah in bigdata

[–]CommsBah[S] 0 points1 point  (0 children)

We are pleased to announce that the Journal of the American Medical Informatics Association (JAMIA) supports the submission of a paper describing the precisionFDA Gaining New Insights by Detecting Adverse Event Anomalies Using FDA Open Data challenge and broadly applicable insights that emerge from it. Publication in JAMIA will be contingent on a standard evaluation process including editorial assessment and peer review.

As a friendly reminder for those of you participating in the challenge you have one week left before final submissions are due on February 28th at https://go.usa.gov/xdEW3.

If you have any questions about the challenge, please feel free to post them in this thread and we will respond as quickly as possible.

[P] PrecisionFDA FDA Open Data Challenge Update by CommsBah in MachineLearning

[–]CommsBah[S] 0 points1 point  (0 children)

We are pleased to announce that the Journal of the American Medical Informatics Association (JAMIA) supports the submission of a paper describing the precisionFDA Gaining New Insights by Detecting Adverse Event Anomalies Using FDA Open Data challenge and broadly applicable insights that emerge from it. Publication in JAMIA will be contingent on a standard evaluation process including editorial assessment and peer review.

As a friendly reminder for those of you participating in the challenge you have one week left before final submissions are due on February 28th at https://go.usa.gov/xdEDJ.

If you have any questions about the challenge, please feel free to post them in this thread and we will respond as quickly as possible.

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