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Computer Innovations Scope

Scope of the Special Journal of Computer Innovations and Bioinformatics [SJ-CIB] defines the extent of what we will publish and what we will not attend to. Thus SJ-CIB will accept within its scope of publication for consideration original and peer-reviewed papers included but not limited to the following list:

Software vulnerabilities

1. Papers that have addressed software vulnerabilities and mitigate security risks dealing with topics such as database management, advanced operating systems, cryptography, and advanced encryption strategies.
2. Papers that outlines how to manage all aspects of an organization’s security, including software applications, networks, storage hardware, devices, and so on.
3. Papers with detailed results on security vulnerabilities scope and the various methods that internal and external attackers use to exploit them.
4. Papers that have policy implications in communication, threat/vulnerability management, knowledge of security compliance rules, and regulations.  

Comprehensive, theory-based applications

1. Papers with a focus on comprehensive, theory-based applications of networking protocols and other aspects of systems design including details on the creation of websites or mobile applications with an emphasis on interface design.
2. Papers outlining the details on how to help an organization make the most of the hardware, software, and services that workers use on a daily basis.
3. Papers on computer products may include but not limited to home-grown systems as well as a wide range of third-party products clearly outlining how main concerns are addressed such as performance, security, and productivity of both the systems themselves as well as the workers using them.

Diagnosing and troubleshooting hardware

1. We expect these papers to assist in designing policies in Diagnosing and troubleshooting hardware and software issues, patching and updating systems, and designing system architecture.
2. Papers that design and create the next generation of computers and technology, clearly showing how we can move beyond the traditional model of a keyboard and monitor to any number of other interfaces such as design thinking and user studies.
3. Papers with details on the many ways that people interact with computers, from websites and mobile phones to voice-enabled speakers and virtual reality.

Interface development and deployment

1. Papers with proof of how effective an interface development and deployment may be and how standard libraries may be used to ensure the compatibility and usability of applications across systems is needed to confirm the originality of such interface. Such papers must have policy implications and must show how knowledge was advanced in: Communication, interpersonal skills, attention to visual detail, mapping how people use software and systems, and so on
2. Papers on programs in software engineering or software theory that usually place a huge emphasis on programming languages for a diversity of uses. These programs naturally emphasize joint teamwork and software security with an emphasis on computer systems, compilers, and databases.

Software engineering research

1. Papers dealing with software engineering research scope with an emphasis on the systems and protocols for using these applications such as debugging and testing, security and scalability, or the ability of an application to add users or features without a negative impact on performance.
2. Such within our scope must advance knowledge in coding and scripting, communication, and collaboration which forms the core interest of the stakeholders such as web Developers, Software Development Engineers and Software Engineer

Computer languages

1. Papers that outlines the key differences between common languages such as JavaScript, Python, Ruby, Visual Basic .NET, SQL, R, and C#.
2. Papers that show knowledge about the types of applications, databases, or other use cases for which each language is best suited.
3. Papers within our scope with details on the use of computer science to advance the knowledge of biological science with an emphasis on how to mine and interpret biological data with cutting edge computerized DNA technologies

Management of massive data sets 

1. Papers within our scope that deal with storage, organization, retrieval, and analysis of massive data sets with detailed emphasis on algorithms for data mining, database architecture, and distributed systems and networking.  
2. Papers on artificial intelligence which deals with probability and modeling, robotics, logical reasoning, natural language processing, and machine learning.

Artificial intelligence

1. Papers that show clearly the applications of artificial intelligence in autonomous cars, data mining and analysis, and intelligent tutoring systems (ITS) will receive preferential attention and consideration.
2. Papers within our scope with details on the computing system’s ability to solve problems, make predictions, or complete complex tasks with emphasis on artificial intelligence applications use emerging technology such as natural language processing, which interprets written and spoken words, and machine learning, which enables applications to make predictions and recommendations.

Algorithms and predictive modeling

1. We expect such papers to advance knowledge in Mathematics and analysis, algorithms, predictive modeling
2. Papers within our scope that deal with realistic images that make computer games appealing and papers that look at the artificial intelligence and machine learning that determines how players progress through a game and also how they work of front-end designers and back-end developers should come together for cohesive product experience.

Bandwidth management and information exchange

1. Papers within our scope that focus on how organizations use both wired and wireless networks to exchange information with internal and external stakeholders with emphasis on managing bandwidth, traffic, user access, and the security of networks themselves, as well as any devices connected to the network.
2. Papers within our scope that focus on two- and three-dimensional images used in many software applications, including games, computer-assisted design, manufacturing, and multimedia publishing with an emphasis on creating realistic images, and also deals with the best way to display those images given limitations such as screen size, system memory, and bandwidth.

Large data mining

1. Papers on data science which deals with the ability to “mine” large data sets to gain useful information or insight. Emphasis should be on Organizational benefit, when a variety of techniques are used to retrieve and analyze data, and when it is used to process large, complex, and sometimes unstructured sets of information.
2. Papers within our scope on advanced mathematical theories and principles that apply to computer science such as advanced cryptography, approximation algorithms, computational algebra, randomness, distributed computing, and parallel computing.

Bioinformatics scope

Genomic data science

• Papers on Genomic Data Science with details on how to better understand the genome, and be able to leverage the data and information from genomic datasets.
• Papers on the concepts and tools to understand, analyze, and interpret data from next-generation sequencing experiments including details showing the most common tools used in genomic data science and how to use the command line, along with a variety of software implementation tools like Python, R, Bioconductor, and Galaxy.
• Papers on how we sequence and compare genomes, How we identify the genetic basis for disease, How we construct an evolutionary Tree of Life for all species on Earth with the ultimate goal of using advanced technologies to better the lives of ordinary people at the grass-root
• Papers on algorithms for solving various biological and programming problems

Algorithms for solving problems

• Papers on algorithmic techniques for solving various computational problems including the implementation of some algorithmic coding problems in a programming language  
• Papers that will show how to design challenges as an alternative to multiple-choice questions and each algorithm developed and implemented, should have designed multiple tests to check its correctness and running time enabling clients to without even knowing what these tests are!
• Papers on how to find optimal efficient algorithms to this P versus NP problems quickly with details on the implementation of several efficient solutions for real-world instances of the traveling salesman problem relying heavily on the proof techniques, combinatorics, probability, graph theory
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Networks research

• Papers on the analysis of both road networks and social networks and depict how to compute the shortest route between major cities and suburbs including how to assemble a genome from millions of short fragments of DNA and how assembly algorithms fuel recent developments in personalized medicine.
• Papers on plant genome sequencing with details on how RNA-seq enabled transcriptome-wide expression profiling, and how the proliferation of “-seq”-based methods allowed for high-throughput and cheap determination of protein-protein and protein-DNA interactions

Hypothesis from databases

• Papers on how These genome data sets allowed for the generation of hypotheses using core bioinformatics competencies and resources, such as NCBI’s Genbank, Blast, multiple sequence alignments, phylogenetics in Bioinformatic Methods I, and protein-protein interaction, structural bioinformatics and RNA-seq analysis in Bioinformatic Methods II.

Plant Bioinformatics

• Papers in Plant Bioinformatics with details in selected online tools such as genome browsers, transcriptomic data mining, promoter/network analyses, and many more.
• Papers on Plant Bioinformatics Capstone that uses Bioinformatics tools to hypothesize a biological role for a gene of unknown function,

Tree Bioinformatics 

• Papers on how to compare genes, proteins, and genomes with details on its use to construct a “Tree of Life” showing how a large collection of related organisms have evolved over time.
• Papers with details on approaches for evolutionary tree construction that have been the subject of some of the most cited scientific papers of all time, and how they can resolve quandaries from finding the origin of a deadly virus to locating the birthplace of modern humans.
• Papers that examine the claim that birds evolved from dinosaurs, its proof may lie on the result that claimed that peptides harvested from a T. Rex Fossil closely matched peptides found in chickens.

Computation proteomics

• Papers on the use of computational proteomics methods to validate results and rule out contamination
• Papers on the application of popular bioinformatics software tools to reconstruct an evolutionary tree of special pathogens of public health importance such as ebolaviruses and identify the source of the recent Ebola epidemic
• Papers on how to identify the function of a protein even if it has been bombarded by so many mutations compared to similar proteins with known functions that it has become barely recognizable as is the case, in HIV studies, since the virus often mutates so quickly that researchers can struggle to study it using a powerful machine learning tool called a hidden Markov model to compare a protein against a related family of proteins.

Comparative genomics

• Papers on how to sequence and compare genomes including how to find mutations lurking within DNA and proteins.
• Papers on how an individual’s genome differs from the “reference genome” of the species including map small fragments of DNA from the individual to the reference genome.
• Papers on elegant and extremely efficient combinatorial pattern matching algorithms require a surprisingly small amount of runtime and memory.
• Papers on the commands that you need to manage and analyze directories, files, and large sets of genomic data.

Bioinformatics and computer programing

• Papers on the Python programming language and the iPython notebook.
• Papers on discrete Math needed to see mathematical structures in the object we work with, and understand their properties and its application in software engineering, data scientists, security and financial analysts including its use in interviews, basic notions and results (combinatorics, graphs, probability, number theory) that are universally needed.
• Papers on the design of systems-level experiments using appropriate cutting edge techniques, collection of big data, and analysis and interpretation of small and big data sets quantitatively.

Bioinformatics and Systems Biology 

• Papers on The Systems Biology with details on the concepts and methodologies used in systems-level analysis of biomedical systems including how to use experimental, computational, and mathematical methods in systems biology and how to design practical systems-level frameworks to address questions in a variety of biomedical fields.

Analytical Bioinformatics

• Papers on how to use tools from the Bioconductor and galaxy project to perform analysis of genomic data.
• Papers on how best to build web applications with JavaScript, HTML, and CSS including the development of web and database applications in PHP, using SQL for database creation, as well as functionality in JavaScript, jQuery, and JSON.

Database design and management

• Papers on basic concepts, like database design, while working on assignments that require the development of increasing challenging web apps from installing a text editor to understanding how a web browser interacts with a webserver to handle events with JQuery,
• Papers on the development of increasingly challenging web sites, and how to demonstrate basic concepts as they are introduced while showcasing competencies in HTML, CSS, PHP, SQL, and JavaScript.
• Papers on how best to use Hadoop with MapReduce, Spark, Pig, and Hive including the use of code, to perform predictive modeling and leverage graph analytics to model problems.
• Papers on how to ask the right questions about data, communicate effectively with data scientists and do basic exploration of large, and complex datasets.