Building on a Legacy : Working with users to revitalize the CRHM hydrological model

A computer scientist's personal account of collaboratively migrating the CRHM hydrological modelling tool.Canada First Research Excellence FundNon-Peer ReviewedA computer scientist's personal account of the challenges involved in collaboratively migrating the CRHM hydrological modelling tool

Reusability Challenges of Scientific Workflows: A Case Study for Galaxy

Scientific workflow has become essential in software engineering because it provides a structured approach to designing, executing, and analyzing scientific experiments. Software developers and researchers have developed hundreds of scientific workflow management systems so scientists in various domains can benefit from them by automating repetitive tasks, enhancing collaboration, and ensuring the reproducibility of their results. However, even for expert users, workflow creation is a complex task due to the dramatic growth of tools and data heterogeneity. Thus, scientists attempt to reuse existing workflows shared in workflow repositories. Unfortunately, several challenges prevent scientists from reusing those workflows. In this study, we thus first attempted to identify those reusability challenges. We also offered an action list and evidence-based guidelines to promote the reusability of scientific workflows. Our intensive manual investigation examined the reusability of existing workflows and exposed several challenges. The challenges preventing reusability include tool upgrading, tool support unavailability, design flaws, incomplete workflows, failure to load a workflow, etc. Such challenges and our action list offered guidelines to future workflow composers to create better workflows with enhanced reusability. In the future, we plan to develop a recommender system using reusable workflows that can assist scientists in creating effective and error-free workflows.Comment: Accepted in APSEC 202

GPTCloneBench: A comprehensive benchmark of semantic clones and cross-language clones using GPT-3 model and SemanticCloneBench

With the emergence of Machine Learning, there has been a surge in leveraging its capabilities for problem-solving across various domains. In the code clone realm, the identification of type-4 or semantic clones has emerged as a crucial yet challenging task. Researchers aim to utilize Machine Learning to tackle this challenge, often relying on the BigCloneBench dataset. However, it's worth noting that BigCloneBench, originally not designed for semantic clone detection, presents several limitations that hinder its suitability as a comprehensive training dataset for this specific purpose. Furthermore, CLCDSA dataset suffers from a lack of reusable examples aligning with real-world software systems, rendering it inadequate for cross-language clone detection approaches. In this work, we present a comprehensive semantic clone and cross-language clone benchmark, GPTCloneBench by exploiting SemanticCloneBench and OpenAI's GPT-3 model. In particular, using code fragments from SemanticCloneBench as sample inputs along with appropriate prompt engineering for GPT-3 model, we generate semantic and cross-language clones for these specific fragments and then conduct a combination of extensive manual analysis, tool-assisted filtering, functionality testing and automated validation in building the benchmark. From 79,928 clone pairs of GPT-3 output, we created a benchmark with 37,149 true semantic clone pairs, 19,288 false semantic pairs(Type-1/Type-2), and 20,770 cross-language clones across four languages (Java, C, C#, and Python). Our benchmark is 15-fold larger than SemanticCloneBench, has more functional code examples for software systems and programming language support than CLCDSA, and overcomes BigCloneBench's qualities, quantification, and language variety limitations.Comment: Accepted in 39th IEEE International Conference on Software Maintenance and Evolution(ICSME 2023

An Exploratory Study to Find Motives Behind Cross-platform Forks from Software Heritage Dataset

The fork-based development mechanism provides the flexibility and the unified processes for software teams to collaborate easily in a distributed setting without too much coordination overhead.Currently, multiple social coding platforms support fork-based development, such as GitHub, GitLab, and Bitbucket. Although these different platforms virtually share the same features, they have different emphasis. As GitHub is the most popular platform and the corresponding data is publicly available, most of the current studies are focusing on GitHub hosted projects. However, we observed anecdote evidences that people are confused about choosing among these platforms, and some projects are migrating from one platform to another, and the reasons behind these activities remain unknown.With the advances of Software Heritage Graph Dataset (SWHGD),we have the opportunity to investigate the forking activities across platforms. In this paper, we conduct an exploratory study on 10popular open-source projects to identify cross-platform forks and investigate the motivation behind. Preliminary result shows that cross-platform forks do exist. For the 10 subject systems in this study, we found 81,357 forks in total among which 179 forks are on GitLab. Based on our qualitative analysis, we found that most of the cross-platform forks that we identified are mirrors of the repositories on another platform, but we still find cases that were created due to preference of using certain functionalities (e.g. Continuous Integration (CI)) supported by different platforms. This study lays the foundation of future research directions, such as understanding the differences between platforms and supporting cross-platform collaboration.Comment: Accepted at 17th International Conference on Mining Software Repositories, October 5--6, 2020, Seoul, Republic of Kore

Antifertility activity of Oroxylum indicum (L.) Kurz:In vitro and in vivo study on human sperm and male wistar rats

Oroxylum indicum (L.) Kurz, commonly called as Broken bones tree or Indian trumpet flower, belonging to Fam. Bignoniaceae, is traditionally used as a contraceptive by ethnic people of Tripura, North-East India. Here, we investigated the scientific basis for use of O. indicum as male antifertility agent by folklore healers. In vitro spermicidal activity of aqueous (AEOI) and methanolic (MEOI) extracts of O. indicum stem bark were studied on human sperm. The in vivo activity was experimented on male albino rats. The treated animals were allowed to mate and the pups delivered by female rat partners were counted. Phytochemical estimation of test samples was done using HPLC. The AEOI and MEOI treatments significantly decreased human sperm motility and viability. Test extracts have increased the hypo-osmotic swelling of sperm. Both the extracts were significantly declined the weight of reproductive organ. The MEOI treated rats have shown significant decrease in sperm motility and sperm counts. AEOI and MEOI treatment significantly reduced level of testosterone, but sharply raised dihydrotestosterone and prostaglandin in rats. Results testified the traditional claim for use of O. indicum as a male contraceptive agent, where MEOI have shown reversible action on male reproductive system leading to contraception without harming the libido

Novel proposals for FAIR, automated, recommendable, and robust workflows

Funding: This work is partly funded by NSF award OAC-1839900. This material is based upon work supported by the U.S. Department of Energy, Office of Science, under contract number DE-AC02-06CH11357. libEnsemble was developed as part of the Exascale Computing Project (17-SC-20-SC), a collaborative effort of the U.S. Department of Energy Office of Science and the National Nuclear Security Administration. This research used resources of the OLCF at ORNL, which is supported by the Office of Science of the U.S. DOE under Contract No. DE-AC05-00OR22725.Lightning talks of the Workflows in Support of Large-Scale Science (WORKS) workshop are a venue where the workflow community (researchers, developers, and users) can discuss work in progress, emerging technologies and frameworks, and training and education materials. This paper summarizes the WORKS 2022 lightning talks, which cover five broad topics: data integrity of scientific workflows; a machine learning-based recommendation system; a Python toolkit for running dynamic ensembles of simulations; a cross-platform, high-performance computing utility for processing shell commands; and a meta(data) framework for reproducing hybrid workflows.Postprin

Damariçi genişleme tedavisi sürecinde stent seçimi için yaklaşim

Son yıllarda medikal uygulamalar da bilgisayar destekli sistemlerin kullanılması giderek yaygınlaşmaktadır. Bu sistemlerin temel amacı, hastaların teşhis ve tedavi sürecinde, uzmanlara daha kaliteli, etkin, doğru ve hızlı bir şekilde destek olmaktır. 3 boyutlu tıbbi görselleştirme, bilgisayar destekli uygulamalarda kullanılan yöntemlerden birisidir. Bu çalışmada abdominal aort anevrizması durumunun tedavisinde uzmana yardımcı olacak bir ölçümleme aracı geliştirilmiştir. Anevrizma tedavisinde kullanılacak olan stentin belirlenmesi amacıyla damar üzerinde farklı ölçümlemeler yapılmaktadır. Bu araç kullanılarak, stent belirlemeye yönelik ölçümler 3 boyutlu ortamda kullanıcı ile etkileşimli olarak gerçekleştirilecektir. Bu çalışmada uzmanların değerlendirme sürecinde kullanmış oldukları Bilgisayar Tomografi görüntüleri incelenerek tıbbi görselleştirme için gerekli aşamalar; bölütleme, kenar belirleme, model oluşturma ve yüzey oluşturma aşamaları gerçekleştirilmiştir. Model üzerinde ölçümlemelerin yapılabilmesi için gerekli dönüşümler yapılarak model kullanıcı ile etkileşimli hale getirilmiştir. Çalışma, yapılan ölçümleme yöntemleri ve yüzey oluşturmadaki çözümleriyle katkı sağlamıştır. Ayrıca Abdomianal Aort Anevrizması tedavisi için özelleştirilmiş bir uygulama geliştirilerek, uzmanların karar verme sürecinde yardımcı olacak bir yazılım sunulmuştur. Çalışma sonucunda ortaya çıkan programın kullanabilirliğini ve doğruluğunu göstermek için; belirli hasta grubuna, geliştirilen program ve manual yöntem ile ölçümlemeler yapılmış ve ölçümleme sonuçları karşılaştırılmıştır. Elde edilen sonuçlar, uygulamanın tutarlı, tekrarlanabilir ve güvenilir sonuçlar ürettiğini göstermiştir. In recent years, usage of computer ? aided systems has been increased tremendously in medical applications. The main purpose of these systems is to support the experts more qualified, efficient, accurate and fast way during patients' diagnosis and treatment. A 3D medical visualization application is one of the areas of computer-aided systems. In this dissertation, a measurement tool is developed to help experts on the treatment of abdominal aortic aneurysm. Different measurements are made on aorta vein to determine which stent?graft is used. The measurements are made with user interaction in 3D environments by the developed application. In this study, Computed Tomography images are examined and necessary steps for medical modeling; segmentation, edge detection, model construction, and surface construction phases are carried out. In order to make interactive measurements on the 3D model, required transformation is applied to the model. Contributions of this study are new surface construction method for tubular structures and measurement methods. Moreover, a new specialized measurement and evaluation tool is developed for abdominal aortic aneurysm. This specialized software will help to medical specialist in decision-making processes. To verify the accuracy and usability of the tool, the measurements are carried out on the selected patients' group by using manual methods and the tool. Obtained statistical results are evaluated and compared. It is proven statistically that the developed tool provides more reliable, more consistent, and more repeatable results