More Like this

1. Automated program repair

   https://doi.org/10.1145/3318162  

   Goues, Claire Le; Pradel, Michael; Roychoudhury, Abhik (November 2019, Communications of the ACM)
2. Program Repair for Hyperproperties

   https://doi.org/10.1007/978-3-030-31784-3_25  

   Bonakdarpour, Borzoo; Finkbeiner, Bernd (October 2019, Automated Technology for Verification and Analysis (ATVA))
3. Folding‐upon‐Repair DNA Nanoswitches for Monitoring the Activity of DNA Repair Enzymes

   https://doi.org/10.1002/ange.202016223  

   Farag, Nada; Mattossovich, Rosanna; Merlo, Rosa; Nierzwicki, Łukasz; Palermo, Giulia; Porchetta, Alessandro; Perugino, Giuseppe; Ricci, Francesco (February 2021, Angewandte Chemie)

   Abstract We present a new class of DNA‐based nanoswitches that, upon enzymatic repair, could undergo a conformational change mechanism leading to a change in fluorescent signal. Such folding‐upon‐repair DNA nanoswitches are synthetic DNA sequences containingO⁶‐methyl‐guanine (O⁶‐MeG) nucleobases and labelled with a fluorophore/quencher optical pair. The nanoswitches are rationally designed so that only upon enzymatic demethylation of theO⁶‐MeG nucleobases they can form stable intramolecular Hoogsteen interactions and fold into an optically active triplex DNA structure. We have first characterized the folding mechanism induced by the enzymatic repair activity through fluorescent experiments and Molecular Dynamics simulations. We then demonstrated that the folding‐upon‐repair DNA nanoswitches are suitable and specific substrates for different methyltransferase enzymes including the human homologue (hMGMT) and they allow the screening of novel potential methyltransferase inhibitors. 

   more » « less
4. Automated model repair for Alloy

   https://doi.org/10.1145/3238147.3238162  

   Wang, Kaiyuan; Sullivan, Allison; Khurshid, Sarfraz (January 2018, 33rd ACM/IEEE International Conference on Automated Software Engineering (ASE))
5. Tortoise: Interactive system configuration repair

   https://doi.org/10.1109/ASE.2017.8115673  

   Weiss, Aaron; Guha, Arjun; Brun, Yuriy (October 2017, Proceedings of the 32nd IEEE/ACM International Conference on Automated Software Engineering (ASE))

   System configuration languages provide powerful abstractions that simplify managing large-scale, networked systems. Thousands of organizations now use configuration languages, such as Puppet. However, specifications written in configuration languages can have bugs and the shell remains the simplest way to debug a misconfigured system. Unfortunately, it is unsafe to use the shell to fix problems when a system configuration language is in use: a fix applied from the shell may cause the system to drift from the state specified by the configuration language. Thus, despite their advantages, configuration languages force system administrators to give up the simplicity and familiarity of the shell. This paper presents a synthesis-based technique that allows administrators to use configuration languages and the shell in harmony. Administrators can fix errors using the shell and the technique automatically repairs the higher-level specification written in the configuration language. The approach (1) produces repairs that are consistent with the fix made using the shell; (2) produces repairs that are maintainable by minimizing edits made to the original specification; (3) ranks and presents multiple repairs when relevant; and (4) supports all shells the administrator may wish to use. We implement our technique for Puppet, a widely used system configuration language, and evaluate it on a suite of benchmarks under 42 repair scenarios. The top-ranked repair is selected by humans 76% of the time and the human-equivalent repair is ranked 1.31 on average. 

   more » « less