Table 1. Availability of the DREAM scoring functions within DREAMTools.
The first column provides the nickname used in DREAMTools to refer to a challenge. The challenge’s title (second column) and its Synapse identifier (fourth column) can be used to retrieve all details about a challenge. The third column gives the challenge status within DREAMTools: most of the challenges’ scoring functions are implemented in DREAMTools (green boxes); open challenges are not yet available (blue boxes); a couple of challenges did not release the gold standard and may not be implemented (red boxes labelled ’No GS’ for no gold standard); some are to be implemented in future releases (orange boxes labelled ’TBD’ for to be done).
| DREAM Nickname | Title | Availability | Synapse ID |
|---|---|---|---|
| D2C1 | BCL6 Transcriptional Target Prediction | Implemented | 3034857 |
| D2C2 | Protein-Protein Interaction Network Inference | Implemented | 2825374 |
| D2C3 | Synthetic Five-Gene Network Inference | Implemented | 3034869 |
| D2C4 | In Silico Network Inference | Implemented | 2825394 |
| D2C5 | Genome-Scale Network Inference | Implemented | 3034894 |
| D3C1 | Signaling Cascade Identification | Implemented | 3033068 |
| D3C2 | Signaling Response Prediction | Implemented | 3825325 |
| D3C3 | Gene Expression Prediction | Implemented | 3033083 |
| D3C4 | In Silico Network | Implemented | 2853594 |
| D4C1 | Peptide Recognition Domain Specificity Prediction | Implemented | 2925957 |
| D4C2 | In silico Network Challenge | Implemented | 2925957 |
| D4C3 | Predictive Signaling Network Modeling | Implemented | 2825304 |
| D5C1 | Epitope-Antibody Recognition Specificity Prediction | Implemented | 2820433 |
| D5C2 | Transcription Factor DNA Motif Recognition | Implemented | 2887863 |
| D5C3 | Systems Genetics Challenge,B | Implemented | 2820440 |
| D5C4 | Network Inference Challenge | Implemented | 2787209 |
| D6C1 | Alternative Splicing | TBD | 2817724 |
| D6C2 | see D7C1 | Implemented | 2841366 |
| D6C3 | Gene Expression Prediction | Implemented | 2820426 |
| D6C4 | FlowCAP2 Molecular Classification of Acute Myeloid LeuKaimia | Implemented | 2887788 |
| D7C1 | Network Topology and Parameter Inference | Implemented | 2821735 |
| D7C2 | Breast Cancer Prognosis | TBD |
2813426
and 1710250 |
| D7C3 | The DREAM Phil Bowen ALS Prediction Prize4Life | Implemented | 2826267 |
| D7C4 | NCI-DREAM Drug Sensitivity | Implemented | 2785778 |
| D8C1 | HPN-DREAM Breast Cancer Network Inference | Implemented | 1720047 |
| D8C2 | NIEHS-NCATS-UNC DREAM Toxicogenetics | Implemented | 1761567 |
| D8C3 | The Whole-Cell Parameter Estimation | TBD | 1876068 |
| D8dot5 | The Rheumatoid Arthritis Responder | Implemented | 1734172 |
| D9C1 | The Broad-DREAM Gene Essentiality Prediction | Implemented | 2384331 |
| D9C2 | Acute Myeloid Leukemia Outcome Prediction | No GS | 2455683 |
| D9C3 | Alzheimer’s Disease Big Data | No GS | 2290704 |
| D9C4 | ICGC-TCGA-DREAM Somatic Mutation Calling | TBD | 312572 |
| D9dot5C1 | Olfactory Challenge | Implemented | 2811262 |
| D9dot5C2 | Prostate Cancer | TBD | 2813558 |
| D10C1 | DREAM ALS Stratification Prize4Life | Open Challenge | 2873386 |
| D10C2 | ICGC-TCGA-DREAM Somatic Mutation Calling Tumor Heterogeneity | Open Challenge | 2813581 |
| D10C3 | ICGC-TCGA DREAM Somatic Mutation Calling RNA Challenge
(SMC-RNA) |
Open Challenge | 2813589 |