# #版本0.99.0 -设置xml文件只有一个单一的约束范畴了。筛选和优化工具逻辑和约束是有区别的访问器。——添加第二舵柄集IGHV——有效性检查设置XML -重新计算所有对比数据分析脚本,底漆视图更新所有情节:覆盖状态取决于方向性现在-添加病毒学的示例应用程序添加覆盖评估# #物流模型版本0.97.0 -重组包添加文档所有功能——修改接口导出功能-写小插图前端文档更新(2016-02-2017)# # # # # 0.9特点:-优化:在研究了高效的启发式集合覆盖独立(Caprari et al。),结果表明二聚作用条件下防止拥有一个高效的拉格朗日启发式引物设计的问题。因此,我们继续使用lpsolve找到一个解决方案独立工党没有任何放松方式。——初始化:底漆初始化运行时和质量有很大的影响的结果。我们之前,天真的引物不允许初始化引物引入模棱两可。因此,我实现了一个基于tree-consensus构造简并引物。这种方法还允许建设的引物只有在高的地区能源节约以减少运行时。-二聚作用:二聚作用计算是非常昂贵的。我看着一个动态规划算法,但事实证明这是非常有用的在我们的场景中,因为它不仅适合彼此子序列的引物。 This isn't the case for us due to our filtering procedure. I should look into other approaches for improving the runtime of dimerization computations at some time. - Updated Dockerfile for new version dependencies - Initialization: changed from RAxML to hclust due to better tree structure. Naive primer sequences are now created for all primers in addition to the degenerate sequences to ensure full coverage of each template by primer candidates. - Optimization: redundant primers are now automatically removed by solving an SCP with the remaining primers and templates with an ILP. - UI: Constraint dependencies are automatically considered when activating/deactivating certain optimization constraints requiring target temperatures (Tm Delta) - Specificity now considers binding to another strand as false positives ## 0.85 ###Features: - New UI: removed clutter; added linear workflows - Changed the definition of GC clamp (has to occur directly at the 3' end and be consecutive) - Added template secondary structure analysis and optimization of template binding region - Allowed region is strict by default now: the primer is not allowed to extend over the allowed region, but there is an option to allow binding if it overlaps the allowed region also. - Partial sequences from IMGT can be removed - Disambiguation of primers - Selection of optimal primer subsets with ILPs - Added plots visualizing constraint values, also for comparing primer sets ###Bug fixes: - Handling of paths with spaces (escapes) for tool installation. However, paths with spaces are still not recommended (doesn't work on mac: libtools) - Reduced the spread of Tm sets such that we have abs(Tm - targetTemperature) <= TmLimit / 2. This limits the maximal melting temperature spread of two primers in a set to TmLimit. ## 0.80 (2016-09-23) ###Features: - Implemented a cancel option for long computations (only integrated into frontend for initialize button yet) - Optimization with linear programs through option in frontend - New dimerization check integrated into frontend - Added license information (GPL v2.0) - Added, but then removed stop buttons for actions in the app (efficiencies couldn't be calculated due to issues with the parallel backend) ###Analyses: - ILP performance - Dimerization validation ###Bug fixes: - Fixed the alignment bug during stop codon check (indels not allowed anymore) and mismatch table - Modified the dimerization constraint of ILPs such that the constraint is alway s pairwise. - Improved the temperature penalty upper bound cutoff value to increase speed of ILP optimization ## 0.75 (2016-07-21) ###Features: - Docker integration with version 0.75 at mdoering88/primer_design - Linear programs backend