NCI-CPTAC DREAM Proteogenomics Challenge

syn8228304

Created By Thomas Yu thomas.yu

Access to original data files
Publication of the results
new metric only changes my team's performance
estimated time to know the scores
No feedback from final write-up submission
Amount of time necessary to validate write-ups
Confusion in final submission or write up submission.
Survey
[Resolved] No email received after final write-up submission
Hongyang Li's round 2 solution and write-up is available
Received error mail after 'Scored' status in sub3 (Breast)
Scoring before final write up
Testing Submissions
Final Write Up due date
[Solved][SC3][Breast] Missing submission in dashboard
No prediction file generated sub2 breast
Suggestions about that 'one missing gene'
[SC2 OVA] SCORED in ex lane, but INVALID in main lane.
[Solved] [SC3-BRCA] Error in main lane / no error in express lane
Missing gold standard samples in RNAseq evaluation data file of leaderboard 1 (SC2 and SC3)
FYI for all participants
Log file request
Submission Dashboard
Proteins to predict for breast cancer data in round 2
Our submission passed SC3 breast ex lane but failed main lane.
Question of SC3 main lane's matrix(rows x columns)
Our submission scored in the express lane but failed in main lane of Sub3 Breast cancer
Our submission passed SC3 ovarian ex lane but failed main lane.
Model passed in SC2 express lane, but failed in main lane
SC3 Breast Express Lane - filename issue
Final submission clarification
Can the organizers clarify this email and re-evaluate round2 and round1 using whatever metrics is going to the end, please?
Update on Phosphosites to be Predicted
SC3 ovarian main lane error.
Validation error on scoring lanes: sub2 and sub3 breast
Elaboration is needed on the final submission instructions
goldstandard proteinIDs donot match between training data and final lane in Proteogenomics Subchallenge 2 Breast
Will the test dataset be made public after the challenge?
Validation error in submission to Proteogenomics Subchallenge 3 Express Lane Ovarian
Suggestions to final submission
Model passed in SC2 express lane, but failed in main lane
Announcment about final round data, partiicapnts please read
model validation error in main queue, but passed in express lane.
Missing sample error SC2_Breast_Express_Lane
[Solved] [SC3] Missing file
NVM
predictions.tsv: All proteinID in the goldstandard must also be in your file
Proteins to be predicted for breast Cancer - SC2
Breast cancer RNAseq file for final test dataset is not found
Breast Cancer Data: Sample IDs
docker size
?? Reporting a minor flaw (potentially without any consequence) in scoring scripts
How do we estimate the submission's running-time(< 10h or 4h)?
SC2: Express lane data
TO use PFS or OS?
Is there anyone also use python?
Whether the scoring script for SC2 is available for us to see?
Main Line submission has been stuck
confidence file must be named confidence.tsv, and your model must generate confidence.tsv
Also got the error in main lane, but not in express lane (sub2)
got the error in main lane, not in express lane (sub2)
score_sc2.sh: pythonscript: not found
SC2: No prediction file generated, please submit to the express lanes to debug your model!
Anyone else having issues contacting the docker daemon while trying to push image?
If you are having trouble with the main lanes please read this!
[Sub1] Error on express lane, but not in main lane
Validation Error SC1 main- Scored in express
Having trouble loading an R-package from CRAN
SC1: Successfully ran express but breaking in main - no logs
SC1 main lane validation fail but scored in express - No prediction file generated
High nrmse score
Information for Round2
Can it be? No more log files for submissions?
About scoring peroid
Error while running submission to Proteogenomics Subchallenge 3
Scoring of SC1 - log file/ status
Can I use matlab script and python script in the same docker image?
About sub challenge 1
Network/ Firewall hangup during cluster making
[subchallenge 2] predictions.tsv: No rows can have variance of 0
Docker push failed
Docker push denied
Submissions per round
No prediction file generated
Sub challenge 1 validation error
Anyone successfully ran in parallel in R?
submissions not processed
Breast Cancer Data
How to parallelize
Round2 Timeline
(Webinar #1) For subchallenge 1, can we borrow information between 10 training datasets to train the prediction function?
how to calculate confidence score for Sub challenge 1?
How will best performers be selected?
i need 16 hours * 16 cores physical not virtual cpus
sort and order command not working while running on Docker.
Any update on leaderboard timeline?
Protein samples for subchallenge 2
What is express lane?
Round one results
Round 2, 3 and Final - data and resources
More technical than scientific
Submission Error: No prediction file generated
Stop the previous submissions.
Question about no output file
4 hours per submission quota is reasonable?
Just missed submission deadline
Corr: nan
Requests to notify all participants when data get updated
Log file --Empty. Submission not updated for several hours.
No logs for invalid submission
Accidentally submitted to the Express Lane as an "Individual"
Submission failing on "predictions file must be named..." [SOLVED, I think..]
Do we have to submit results in every round to get ranked in the final round?
Docker push problems
Docker server is down?
Keep getting "/score_sc2.sh: ... Killed" errors in Sub-Challenge 2 submission
Extremely slow compute resources
[subchallenge 2] order of the proteins in the prediction file
No scored result mail in SC2 and SC3
Check status of code
How to stop previous submissions
Installing specific version of R in linux
(Webinar #1) Do we have to make our first submission before round 1 ends?
Submission to express lane status: Scored, in main lane: Invalid
Subchallenge 2 training data
Has anyone successfully submitted a MATlab script with Docker?
Error submitting SC1 express
will the round1 data be released after round1 ends
[Solved] SC3 express lane submission error
SC2 express lane data import error _ issue resolved
Submissions
Grabbing data script
SC3 the phosphosites
SC1 Validation Error on Express Lane
Question about submission of expression lane.
Are /evaluation_data/data_test_obs_*.txt files present in SubChallenge1 Express Lane?
Docker tutorial and examples of submission scripts
Submission to challenge 2 express lane
About sub-challenge 2
Submission to express lane
How to validate docker submission?
How to Download the data?
subset of proteins that should be scored ? (Sub2)
Question about using MATLAB scripts
3.3 - Accessing Data UPDATE
(Webinar #1) What is the number of allowable submissions for each subchallenge?
Question about matrix of test data
(Webinar #1) What are the zeros in data_true.txt for challenge 1?
Running parallelization inside submitted docker
Question about submission of this challenge.
(Webinar #1) Is it possible to submit docker projects to a sandbox to see if everything is working?
Which lineage will the test data come from? [ Sub-challenge 2]
Log File Restrictions
Extremely High Correlation Observed in Sub1
Is my understanding correct about Subchallenge 1?
Do the test examples change between phases of the leaderboard?
(Webinar #1) Why is there an additional proteomic dataset for ovarian cancer in sc3 (JHU / NPPL) ?
Aren't we just learning the simulation model in subchallenge 1?
(Webinar #1) Will experimental variables, mass to charge ratio and tag id be available?
(Webinar #1) What is the deadline for submissions in the round 1?
(Webinar #1) What are the allowed function runtimes for each subchallenge?
(Webinar #1) Docker integration appears to still be in beta. Is it fully functional? Is it stable?
(Webinar #1) Where does google compute engine come in?
(Webinar #1) Can we use external data?
(Webinar #1) If our scripts rely on a local database, is there a limit on the docker size?
RNA-seq data
NVM
Docker Push (unauthorized: authentication required)
Sample Annotation Questions
Confidence file for subchallenge 2 and 3
Sub Task 2 : about missing protein values.
Looking for a team!
Docker
How are the sub-challenges weighted?
Data description, subchallenge 2
What is Round1, Round2,Round3 in Leaderboard Phase mean?
Sub-challenge 1: data_true 0s simulated using bernoulli p =.1, data_obs NAs simulated with exactly 1/3 being 0
Subchallenge 1: Question on simulated zeros.
CNA file has duplicate rows?
Looking for a team
Row header(Gene_ID) mismatch in sub_challenge 3
Sub1, reproducing zeros in the ground truth
Right way to train and test for Sub challenge 1.
Use of External Data in sub-challenge 2
Scoring function with zeros values as normalization
test data, sub 1 chanllenge
Round system and number of submissions per team
Data Description, Subchallenge 1
Looking for a Team (with meetup at ISMB/ECCB 2017 in Prague?)
Mismatching sample header for Subchallenge 2, breast cancer
Anyone interested to take me as a part of team
Description of data
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