macOS Systems Research Articles

Uncovering security vulnerabilities through multiplatform malware analysis

AbstractCybercriminals, keen on staying anonymous, focus on creating secure connections to hide their activities. This has fueled the rise of malware, especially remote access trojans (RATs), designed to protect themselves for long‐term use and profit. This research investigates how multiplatform malware analysis can expose security weaknesses across Windows, Linux, and macOS systems. We designed and analyzed custom malware to uncover vulnerabilities that attackers could exploit to establish persistent, hidden access. The malware was programmed to bypass detection while performing actions like stealing sensitive data, launching denial‐of‐service attacks, and generating fake website traffic. Controlled lab experiments and real‐world simulations confirmed the malware's ability to operate stealthily on various platforms, highlighting critical security gaps. By uncovering these vulnerabilities, this study provides valuable insights for strengthening cybersecurity defenses.

Tissue Forge: Interactive biological and biophysics simulation environment.

Tissue Forge is an open-source interactive environment for particle-based physics, chemistry and biology modeling and simulation. Tissue Forge allows users to create, simulate and explore models and virtual experiments based on soft condensed matter physics at multiple scales, from the molecular to the multicellular, using a simple, consistent interface. While Tissue Forge is designed to simplify solving problems in complex subcellular, cellular and tissue biophysics, it supports applications ranging from classic molecular dynamics to agent-based multicellular systems with dynamic populations. Tissue Forge users can build and interact with models and simulations in real-time and change simulation details during execution, or execute simulations off-screen and/or remotely in high-performance computing environments. Tissue Forge provides a growing library of built-in model components along with support for user-specified models during the development and application of custom, agent-based models. Tissue Forge includes an extensive Python API for model and simulation specification via Python scripts, an IPython console and a Jupyter Notebook, as well as C and C++ APIs for integrated applications with other software tools. Tissue Forge supports installations on 64-bit Windows, Linux and MacOS systems and is available for local installation via conda.

Discovering spoliation of evidence through identifying traces on deleted files in macOS

Spoliation of evidence is a critical concern in various crimes such as information leakage, digital sexual crimes, accounting fraud, and copyright infringement. Several traditional digital forensic investigation methods such as recovery, carving, and anti-forensic behavior tracking are used to investigate these crimes. However, as technology has advanced, recovery and carving have become increasingly challenging. Shortly, data recovery will reach its technological limit, and it will be essential to obtain as much circumstantial evidence as possible based on traces of data left in suspect systems. However, no existing method can systematically track the spoliation of evidence; contemporary investigations typically depend solely on investigators’ skills and knowledge. This paper proposes a method to track deleted files by identifying and analyzing various sources that manage file-related metadata in macOS systems.

Findzx: an automated pipeline for detecting and visualising sex chromosomes using whole-genome sequencing data

BackgroundSex chromosomes have evolved numerous times, as revealed by recent genomic studies. However, large gaps in our knowledge of sex chromosome diversity across the tree of life remain. Filling these gaps, through the study of novel species, is crucial for improved understanding of why and how sex chromosomes evolve. Characterization of sex chromosomes in already well-studied organisms is also important to avoid misinterpretations of population genomic patterns caused by undetected sex chromosome variation.ResultsHere we present findZX, an automated Snakemake-based computational pipeline for detecting and visualizing sex chromosomes through differences in genome coverage and heterozygosity between any number of males and females. A main feature of the pipeline is the option to perform a genome coordinate liftover to a reference genome of another species. This allows users to inspect sex-linked regions over larger contiguous chromosome regions, while also providing important between-species synteny information. To demonstrate its effectiveness, we applied findZX to publicly available genomic data from species belonging to widely different taxonomic groups (mammals, birds, reptiles, and fish), with sex chromosome systems of different ages, sizes, and levels of differentiation. We also demonstrate that the liftover method is robust over large phylogenetic distances (> 80 million years of evolution).ConclusionsWith findZX we provide an easy-to-use and highly effective tool for identification of sex chromosomes. The pipeline is compatible with both Linux and MacOS systems, and scalable to suit different computational platforms.

ITaxoTools 0.1: Kickstarting a specimen-based software toolkit for taxonomists

While powerful and user-friendly software suites exist for phylogenetics, and an impressive cybertaxomic infrastructure of online species databases has been set up in the past two decades, software targeted explicitly at facilitating alpha-taxonomic work, i.e., delimiting and diagnosing species, is still in its infancy. Here we present a project to develop a bioinformatic toolkit for taxonomy, based on open-source Python code, including tools focusing on species delimitation and diagnosis and centered around specimen identifiers. At the core of iTaxoTools is user-friendliness, with numerous autocorrect options for data files and with intuitive graphical user interfaces. Assembled standalone executables for all tools or a suite of tools with a launcher window will be distributed for Windows, Linux, and Mac OS systems, and in the future also implemented on a web server. The initial version (iTaxoTools 0.1) distributed with this paper (https://github.com/iTaxoTools/iTaxoTools-Executables) contains graphical user interface (GUI) versions of six species delimitation programs (ABGD, ASAP, DELINEATE, GMYC, PTP, tr2) and a simple threshold-clustering delimitation tool. There are also new Python implementations of existing algorithms, including tools to compute pairwise DNA distances, ultrametric time trees based on non-parametric rate smoothing, species-diagnostic nucleotide positions, and standard morphometric analyses. Other utilities convert among different formats of molecular sequences, geographical coordinates, and units; merge, split and prune sequence files, tables and species partition files; and perform simple statistical tests. As a future perspective, we envisage iTaxoTools to become part of a bioinformatic pipeline for next-generation taxonomy that accelerates the inventory of life while maintaining high-quality species hypotheses. The open source code and binaries of all tools are available from Github (https://github.com/iTaxoTools) and further information from the website (http://itaxotools.org).

SPDE: a multi-functional software for sequence processing and data extraction.

Sequence Processing and Data Extraction (SPDE) has eight modules comprising 100 basic functions ranging from sequence extraction, format conversion to data reorganization and mining, and all of these functions can be completed by point-and-click icons. SPDE also incorporates eight public analyses tools; thus, SPDE is a comprehensive bioinformatics platform for big biological data analysis. SPDE built by Python can run on 32-bit, 64-bit Windows and MacOS systems. It can be downloaded from https://github.com/simon19891216/SPDEv1.2.git. Supplementary data are available at Bioinformatics online.

BootBandit: A macOS bootloader attack

Historically, the boot phase on personal computers left systems in a relatively vulnerable state. Because traditional antivirus software runs within the operating system, the boot environment is difficult to protect from malware. Examples of attacks against bootloaders include so‐called “evil maid” attacks, in which an intruder physically obtains a boot disk to install malicious software for obtaining the password used to encrypt a disk. The password then must be stored and retrieved again through physical access. In this paper, we discuss an attack that borrows concepts from the evil maid. We assume exploitation can be used to infect a bootloader on a system running macOS remotely to install code to steal the user's password. We explore the ability to create a communication channel between the bootloader and the operating system to remotely steal the password for a disk protected by FileVault 2. On a macOS system, this attack has additional implications due to “password forwarding” technology, in which a user's account password also serves as the FileVault password, enabling an additional attack surface through privilege escalation.

Pblat: a multithread blat algorithm speeding up aligning sequences to genomes

BackgroundThe blat is a widely used sequence alignment tool. It is especially useful for aligning long sequences and gapped mapping, which cannot be performed properly by other fast sequence mappers designed for short reads. However, the blat tool is single threaded and when used to map whole genome or whole transcriptome sequences to reference genomes this program can take days to finish, making it unsuitable for large scale sequencing projects and iterative analysis. Here, we present pblat (parallel blat), a parallelized blat algorithm with multithread and cluster computing support, which functions to rapidly fine map large scale DNA/RNA sequences against genomes.ResultsThe pblat algorithm takes advantage of modern multicore processors and significantly reduces the run time with the number of threads used. pblat utilizes almost equal amount of memory as when running blat. The results generated by pblat are identical with those generated by blat. The pblat tool is easy to install and can run on Linux and Mac OS systems. In addition, we provide a cluster version of pblat (pblat-cluster) running on computing clusters with MPI support.Conclusionpblat is open source and free available for non-commercial users. It is easy to install and easy to use. pblat and pblat-cluster would facilitate the high-throughput mapping of large scale genomic and transcript sequences to reference genomes with both high speed and high precision.

The Webometrics Analysis of Market Share and Network Attention of Operation Systems for Personal Computers - Based on the Baidu Index as a Web Metrics Research

This paper explores the relationship between network attention and market share of operation systems for personal computers using webometrics. Results show that market share of XP and Win7 network attention, Win7 market share are both negatively strong correlated, while Win7 market share and network attention exhibit a strong positive correlation. Win7 market share and Mac OS market is positive correlated, from which we can infer that Win7 operating system is often used to query the Mac OS when users are confronted with related problems. Market attention of Mac OS operating system and other operating system has no significant correlation, which shows that the Mac OS system is different from other operating systems with relative independence. Finally, based on the differences between positive correlation and negative correlation, referential suggestions are provided for the technology innovation and development of the operating system.

Anomaly Detection Based on Chi-Square Statistic Technology in Computer Information System

Algorithm and principle of anomaly detection technique based on a chi-square statistic was designed. In order to verify the effect of principle and algorithm, testing data of sample of Windows7 and Mac OS system was presented and compared. The results of this study show that chi-square technology achieves the 0% false alarm rate and the 100% detection rate for abnormal intrusion scenarios. All intrusion scenarios are detected at the first or second audit event.

PIPHULA—parallel inference of population parameters using a likelihood approach

pIPHULA is the parallel program to estimate the parameters of a realistic model of population growth.

In silico sequence evolution with site-specific interactions along phylogenetic trees

A biological sequence usually has many sites whose evolution depends on other positions of the sequence, but this is not accounted for by commonly used models of sequence evolution. Here we introduce a Markov model of nucleotide sequence evolution in which the instantaneous substitution rate at a site depends on the states of other sites. Based on the concept of neighbourhood systems, our model represents a universal description of arbitrarily complex dependencies among sites. We show how to define complex models for some illustrative examples and demonstrate that our method provides a versatile resource for simulations of sequence evolution with site-specific interactions along a tree. For example, we are able to simulate the evolution of RNA taking into account both secondary structure as well as pseudoknots and other tertiary interactions. To this end, we have developed a program Simulating Site-Specific Interactions (SISSI) that simulates evolution of a nucleotide sequence along a phylogenetic tree incorporating user defined site-specific interactions. Furthermore, our method allows to simulate more complex interactions among nucleotide and other character based sequences. We implemented our method in an ANSI C program SISSI which runs on UNIX/Linux, Windows and Mac OS systems, including Mac OS X. SISSI is available at http://www.bi.uni-duesseldorf.de/software/sissi/

A multimodal data collection tool using REALbasic and Mac OS X.

This project uses REALbasic 3.5 in the Mac OS X environment for development of a configuration tool that builds a data collection procedure for investigating the effectiveness of sonified graphs. The advantage of using REALbasic with the Mac OS X system is that it provides rapid development of stimulus presentation, direct recording of data to files, and control over other procedural issues. The program can be made to run natively on the new Mac OS X system, older Mac OS systems, and Windows (98SE, ME, 2000 PRO). With modification, similar programs could be used to present any number of visual/auditory stimulus combinations, complete with questions for each stimulus.