Assessing and assuring interoperability of a genomics file format

Background: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Methods: We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing interoperability. As a focus, we selected the popular BED file format for genomic interval data. Based on the file format's original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing. Results: Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. Discussion: Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.

Optimum Test Suite using Fault-Type Coverage Based Ant Colony Optimization Algorithm

Software Product Lines(SPLs) covers a mixture of features for testing Software Application Program(SPA). Testing cost reduction is a major metric of software testing. In combinatorial testing(CT), maximization of fault type coverage and test suite reduction plays a key role to reduce the testing cost of SPA. Metaheuristic Genetic Algorithm(GA) do not offer best outcome for test suite optimization problem due to mutation operation and required more computational time. So, Fault-Type Coverage Based Ant Colony Optimization(FTCBACO) algorithm is offered for test suite reduction in CT. FTCBACO algorithm starts with test cases in test suite and assign separate ant to each test case. Ants elect best test cases by updating of pheromone trails and selection of higher probability trails. Best test case path of ant with least time are taken as optimal solution for performing CT. Hence, FTCBACO Technique enriches reduction rate of test suite and minimizes computational time of reducing test cases efficiently for CT.

An Effective Approach to Test Suite Reduction and Fault Detection Using Data Mining Techniques

Software testing is used to find bugs in the software to provide a quality product to the end users. Test suites are used to detect failures in software but it may be redundant and it takes a lot of time for the execution of software. In this article, an enormous number of test cases are created using combinatorial test design algorithms. Attribute reduction is an important preprocessing task in data mining. Attributes are selected by removing all weak and irrelevant attributes to reduce complexity in data mining. After preprocessing, it is not necessary to test the software with every combination of test cases, since the test cases are large and redundant, the healthier test cases are identified using a data mining techniques algorithm. This is healthier and the final test suite will identify the defects in the software, it will provide better coverage analysis and reduces execution time on the software.

Một số cải tiến cho các kiểm tra thống kê tính ngẫu nhiên sử dụng so khớp mẫu

Tóm tắt—Các kiểm tra liên quan đến so khớp mẫu chồng lấp đã được đề xuất trong NIST SP 800-22 [1], tuy nhiên các xác suất trong các kiểm tra này chỉ đúng cho các mẫu đặc biệt và cần được tính lại cho các mẫu khác. Trong [2], các tác giả đã đề xuất các tiêu chuẩn thống kê so khớp mẫu mới cho tất cả các mẫu 4 bit. Các kiểm tra mới này áp dụng cho chuỗi bất kỳ có độ dài tối thiểu là 5504 bit, trong khi theo NIST độ dài tối thiểu 106 bit. Trong bài báo này, chúng tôi đã cải tiến và đề xuất các kiểm tra so khớp mẫu 4 bit mới mà có thể áp dụng cho các chuỗi bất kỳ có độ dài nhỏ nhất chỉ là 3726 bit. Hơn nữa, chúng tôi đưa ra 3 kiểm tra thống kê so khớp mẫu 5 bit mới. Kết quả lý thuyết và thực hành cho thấy các đề xuất cải tiến của chúng tôi là rất hiệu quả trong việc đánh giá tính ngẫu nhiên cho các bộ tạo số giả ngẫu nhiên. Abstract—Randomness tests related to overlapping template matching have been proposed in NIST SP 800-22 [1], however the probabilities in these tests are only valid for specific samples and should be recalculated for other samples. In [2], the authors proposed new template matching tests for all 4-bit templates. The new tests can be applied to any sequence of minimum length of 5504 bits whereas the overlapping template matching test in the NIST test suite can only be applied to sequences of minimum length of 106 bits. In this paper, we have modified and proposed new 4-bit template matching tests that can be applied to any sequence of minimum length 3726 bits. Furthermore, we proposed three new 5-bit template matching tests. Our theoretical and practical results show that our new proposed tests are very efficient in psedorandom number generator testing.

Mối liên hệ giữa tính nhận biết tiền ảnh và một số tính chất mật mã khác của hàm băm

Tóm tắt—Các kiểm tra liên quan đến so khớp mẫu chồng lấp đã được đề xuất trong NIST SP 800-22 [1], tuy nhiên các xác suất trong các kiểm tra này chỉ đúng cho các mẫu đặc biệt và cần được tính lại cho các mẫu khác. Trong [2], các tác giả đã đề xuất các tiêu chuẩn thống kê so khớp mẫu mới cho tất cả các mẫu 4 bit. Các kiểm tra mới này áp dụng cho chuỗi bất kỳ có độ dài tối thiểu là 5504 bit, trong khi theo NIST độ dài tối thiểu 106 bit. Trong bài báo này, chúng tôi đã cải tiến và đề xuất các kiểm tra so khớp mẫu 4 bit mới mà có thể áp dụng cho các chuỗi bất kỳ có độ dài nhỏ nhất chỉ là 3726 bit. Hơn nữa, chúng tôi đưa ra 3 kiểm tra thống kê so khớp mẫu 5 bit mới. Kết quả lý thuyết và thực hành cho thấy các đề xuất cải tiến của chúng tôi là rất hiệu quả trong việc đánh giá tính ngẫu nhiên cho các bộ tạo số giả ngẫu nhiên. Abstract—Randomness tests related to overlapping template matching have been proposed in NIST SP 800-22 [1], however the probabilities in these tests are only valid for specific samples and should be recalculated for other samples. In [2], the authors proposed new template matching tests for all 4-bit templates. The new tests can be applied to any sequence of minimum length of 5504 bits whereas the overlapping template matching test in the NIST test suite can only be applied to sequences of minimum length of 106 bits. In this paper, we have modified and proposed new 4-bit template matching tests that can be applied to any sequence of minimum length 3726 bits. Furthermore, we proposed three new 5-bit template matching tests. Our theoretical and practical results show that our new proposed tests are very efficient in psedorandom number generator testing.

Comparison of Multi-Objective Evolutionary Algorithms to Prioritize Regression Test Cases

Regression testing is one of the most critical testing activities among software product verification activities. Nevertheless, resources and time constraints could inhibit the execution of a full regression test suite, hence leaving us in confusion on what test cases to run to preserve the high quality of software products. Different techniques can be applied to prioritize test cases in resource-constrained environments, such as manual selection, automated selection, or hybrid approaches. Different Multi-Objective Evolutionary Algorithms (MOEAs) have been used in this domain to find an optimal solution to minimize the cost of executing a regression test suite while obtaining maximum fault detection coverage as if the entire test suite was executed. MOEAs achieve this by selecting set of test cases and determining the order of their execution. In this paper, three Multi Objective Evolutionary Algorithms, namely, NSGA-II, IBEA and MoCell are used to solve test case prioritization problems using the fault detection rate and branch coverage of each test case. The paper intends to find out what’s the most effective algorithm to be used in test cases prioritization problems, and which algorithm is the most efficient one, and finally we examined if changing the fitness function would impose a change in results. Our experiment revealed that NSGA-II is the most effective and efficient MOEA; moreover, we found that changing the fitness function caused a significant reduction in evolution time, although it did not affect the coverage metric.

Detecting security vulnerabilities with static analysis – A case study

Many security vulnerabilities can be detected by static analysis. This paper is a case study and a performance comparison of four open-source static analysis tools and plugins (PMD, SpotBugs, Find Security Bugs, and SonarQube) on Java source code. Experiments have been conducted on the widely used Juliet Test Suite with respect to six selected weaknesses from the official Top 25 list of Common Weakness Enumeration. In this study, analysis metrics have been calculated for helping Java developers decide which tools can be used when checking their programs for security vulnerabilities. It turned out that particular weaknesses are best detected with particular tools.