ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge


Created By Robert Küffner KROBERT

Will all binding data be available soon?
raw RNA-seq data
About the TF/celltype score
Main paper status update
Status on the paper
Write-up and Code Submission
Benchmarking Phase File Naming Conventions
Benchmark round data
Synapse Page etc
Extension on write-up?
final submission error
Final Submission error: "The reference file has more rows than the reference file"
Final submissions
Deadline Method Write-up and Code Delivery
Syanpse Q
Strange scores
Can't submit as a team
Scoring Scripts
Submssion not returned
Qualification of Being Part of the Community
On Chip-seq data
Possible issue with Leaderboard submissions
File download error
Final submission deadline
Model based on already published tools
Submissions not being scored.
Show ranking again?
Tips for combining cell lines?
Sequence conservation
After completion of second round
Inconsistency with IMR90 naming
I'm releasing my CNN code
Advantages of using BAM vs. bigWig for DNase features?
Extracting Training Sequences as FASTA
Dissemination of the winning methods
Presentations at the DREAM conference
Broken links
DNase-seq FC bigWig generation procedure?
Is it too late to join the contest
Can We Use Challenge Data for academic purposes
DNase-seq data processing
Phase 2 Live!!
liver DNase data low quality?
Multi-task training
ENCODE-DREAM Challenge Phase 2
Conflicting Submission
Finding a good architecture and parameters for convolutional neural networks
Consider changing the chromatin accessibility figure?
TAF1 final scores
Conference Round Results
Dnase signal normalization
Leaderboard re-open for round 2
Question about CHIP-seq Fold-enrichment signal coverage tracks
liver & induced_pluripotent_stem_cell cell types
A note to teams that made final submissions
Failed Submission
Write up
Final round submission status
Line 1 in submitted file does not conform to the required pattern: '(\S+ \d+ \d+) (\S+)
FINAL Deadline extension to Tuesday, Oct 4 11.59 pm Pacific time.
Final Submission Round Update
Final submission 6 hours ago, not any email notification yet
Chrome upload speed: 800kb/s; BUT FireFox is 2MB/s.
Final round submissions
Final Submission Status
"Has a conflicting submission" as a team
Question about queue
Waiting response on the submissions
Missing Leaderboard Ranking?
An inunderstandable error message
unable to submit to final leaderboard
Team members are ineligible to contribute to a Submission in the specified Evaluation at this time [3344506]
Can we make submissions now?
Leaderboard submissions got lost [false alarm?]
Still have the naming issue: does not match expected naming pattern '[0-9\.]*([LFB])\.(.+?)\.(.+?).tab.gz$'
A Repeated Submission and Naming Issue Still
Mistaken submission as "individual"
Final Round deadline extension (Sunday Oct 2 2016, midnight Pacific Time)
Delay in Scoring Leaderboard Submissions
Submission evaluation
Issue with submitting to challenge
Submission queue id for final submission?
Rank of all the team
i can upload any file, but not the submission file.
ChIP-seq peaks vs DNase hypersensitive regions
Conference Round closes Sept 30, challenge will be extended until January 7, 2017.
DO we have to submit for every TF in order to be part of ENCODE-DREAM Community co-author?
Final Submission Queues Open!!! Additional notes on the Challenge
Gene Annotation and Gene Set Information Allowed to be Used?
State of file
genes that affecting TF binding
submission not showing - leaderboard
Unified scoring active on Leaderboard
What does rank -1 mean?
duplicated submission
Multiple identical submissions
Pulling/parsing training examples efficiently. Anyone using Convolutional neural networks?
i cant upload predictions on leaderboard round
The score of the base model
Tools to predict DNA Methylation just using DNA sequence
Destination directory for download script
Question on Final Submission Evaluation
Using PBM scores
predictions > 1
Indexing ChIP tsv label files for rapid retrieval
Energy model Motif scanning
The final submission round is ahead and just
Useful resource for DNAshape
Using known motifs?
Features from raw Chip Peaks
Are there any fixed time-limits or time estimates to score a particular submission?
[edit: false alarm, please ignore] Scoring script bug?
Synapse id of the evaluation for the challenge
Hg19/GRCh37 genome sequence
Ensembl Gene Ids in RNAseq data are missing in Ensembl BioMart downloaded mappings
ChIP peak file format
Duplicated DNase peaks?
FDR cut-offs
if this is really a scoring bug, would i be given a by-line coauthorship?
data on chrX/Y/M
Is there a proper way to change from a single submitter to a team?
DNase bam files
EP300 and TAF1 motifs
Instructions for batch uploading of submissions
Flach and Kull AUPRG statistics
baseline and HMMs
Scoring is Live!!
Can I use histone modification data derived features ?
WEBINAR presentation and answers to question
Slides from webinar
Changing from single submitter to team
Histone modifications
Is liver a true blind cell type for ATF3?
DNA Shape
X% FDR procedure.
Any team need a team-mate?
TF binding Prediction Files
ATF7 in data table but not in Factorbook
Challenge Webinar July 22.
MonBUG hackathon in the Old Port of Montreal
How were the fold-enrichment tracks generated?
incompatible values in fc.signal.bigwig
download error
Question about files
Got error while downloading datga using python script
same here: recruit teammate(s) for this challenge
Download data fail by using python script.
So the Conservation peaks are subsets of relaxed peaks?
Unable to download data
What will the final output look like?
When will the data be posted?

ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge page is loading…