SPADA Docs

most computational models of PCR perform satisfactorily within the “well-behaved” limits of 615 perfect match primers, short amplicons, no-template near neighbors, and single-plex PCR, many 616 real-world applications do not fall into this category. Thus, a “ground truth” dataset is needed to 617 help determine model accuracy. The dataset could be used to objectively evaluate algorithms 618 from different research groups. The experimental, “ground truth” PCR dataset would need to 619 capture many details including: (a) the target genome, (b) the presence of contaminating 620 organisms (determined through NGS sequencing), (c) the enzyme and buffer compositions, (d) 621 the primer and probe concentrations, (e) the composition of the amplicon products (by NGS 622 sequencing to reveal the concentrations of the desired amplicon and off-target amplicons, primer 623 dimers, etc.), and (f) the composition of the PCR reaction at each cycle of PCR (e.g., real time 624 monitoring of the fluorescence, along with quantification of primer concentrations and enzyme 625 activity). For this training dataset (no publicly available dataset), both the PCR inputs and 626 outputs would be publicly revealed to enable the user community to improve and validate their in 627 silico methods. 628 629 5.3 PCR Datasets in Support of Competitions to Spur the Community Forward 630 631 an open competition to assess the performance of different computational approaches for in 632 silico PCR using experimental data. Competitions could provide a quantitative ranking of models 633 by accuracy and spur the development of improved in silico models. In particular, to rigorously 634 compare different in silico prediction methods, it would be important to experimentally explore 635 "bad" real-time PCR assays, including: 1) amplicons that are too long; 2) amplicons with strong 636 secondary structure; 3) mismatches in both the forward and reverse primers; and 4) varying 637 Similar to the Critical Assessment of Protein Structure Prediction (CASP), there is a need for

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