Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Automatic Detection of Public Development Projects in Large Open Source Ecosystems: An Exploratory Study on GitHub

Hosting over 10 million of software projects, GitHub is one of the most important data sources to study behavior of developers and software projects. However, with the increase of the size of open source datasets, the potential threats to mining these datasets have also grown. As the dataset grows, it becomes gradually unrealistic for human to confirm quality of all samples. Some studies have investigated this problem and provided solutions to avoid threats in sample selection, but some of these solutions (e.g., finding development projects) require human intervention. When the amount of data to be processed increases, these semi-automatic solutions become less useful since the effort in need for human intervention is far beyond affordable. To solve this problem, we investigated the GHTorrent dataset and proposed a method to detect public development projects. The results show that our method can effectively improve the sample selection process in two ways: (1) We provide a simple model to automatically select samples (with 0.827 precision and 0.947 recall); (2) We also offer a complex model to help researchers carefully screen samples (with 63.2% less effort than manually confirming all samples, and can achieve 0.926 precision and 0.959 recall).Comment: Accepted by the SEKE2018 Conferenc

A Quantitative Study of Java Software Buildability

Researchers, students and practitioners often encounter a situation when the build process of a third-party software system fails. In this paper, we aim to confirm this observation present mainly as anecdotal evidence so far. Using a virtual environment simulating a programmer's one, we try to fully automatically build target archives from the source code of over 7,200 open source Java projects. We found that more than 38% of builds ended in failure. Build log analysis reveals the largest portion of errors are dependency-related. We also conduct an association study of factors affecting build success

Evaluating Maintainability Prejudices with a Large-Scale Study of Open-Source Projects

Exaggeration or context changes can render maintainability experience into prejudice. For example, JavaScript is often seen as least elegant language and hence of lowest maintainability. Such prejudice should not guide decisions without prior empirical validation. We formulated 10 hypotheses about maintainability based on prejudices and test them in a large set of open-source projects (6,897 GitHub repositories, 402 million lines, 5 programming languages). We operationalize maintainability with five static analysis metrics. We found that JavaScript code is not worse than other code, Java code shows higher maintainability than C# code and C code has longer methods than other code. The quality of interface documentation is better in Java code than in other code. Code developed by teams is not of higher and large code bases not of lower maintainability. Projects with high maintainability are not more popular or more often forked. Overall, most hypotheses are not supported by open-source data.Comment: 20 page