Assessment: Tool Kit for Bioinformatics

Assessment 3 Instructions: Tool Kit for Bioinformatics

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Assessment 3 Instructions: Tool Kit for Bioinformatics

Bioinformatics refers to the application of computational and analysis tools to gather and interpret biological or clinical data. Bioinformatics approaches are necessary for the management of modern clinical biology and medicine. Bioinformatics often involves the application of a toolbox that has to be fully integrated with all the required components. Some of these components include computer applications such as Ensembl and BLAST, which rely on the availability of the internet (Baxevanis et al., 2020). Bioinformatics has been used in different healthcare processes. For instance, examination/analysis of genome sequence data, especially the analysis of human genome projects, depends entirely on the bioinformatics approaches. Some of the prospects in the field of bioinformatics include the future contribution to the functional understanding of human genomes. Bioinformatics is essential because of its future contribution to the functional understanding of the human genome, a scenario that is likely to enhance the discovery of different individualized therapy and the enhanced discovery of drug targets.

Bioinformatics Tool Kit

A tool kit for implementing bioinformatics in an organization should incorporate different factors. The toolkit should consist of a wide array of standalone applications and toolkit libraries for bioinformatics. The toolkit ought to incorporate Java. The Java application is particularly good in the provision of the graphical user interfaces using platform-agnostic. Early forms of java development Kits were regarded as inconvenient for transferring text-oriented files; however, the incorporation of straightforward regular expression tools such as JDK and API has increased the efficiency of implementing different tasks in bioinformatics for the less experienced programmers (Chen et al., 2019). Java tool continues to enjoy increased popularity in bioinformatics for developing applications from the reusable component libraries. The toolkit should have object-relational bridges to BioSQL capable of binding objects in the model of data of the respective toolkit in line with the corresponding tables/entities within the relational model (Roumpeka et al., 2017). The bioinformatics schema ought to be moderately simple, with less than thirty tables in total.

An Evidence-Based Policy That Explains What Is To Be Done and Why

The bioinformatics toolkit should be designed in line with the evidence-based policies that guide data and information systems. Transforming the quality of healthcare is essential for effective patient outcomes. Research is one of the evidence-based policies that can guide the application of different approaches in the implementation and application of bioinformatics tools. The evidence-based practice should also involve the consideration of ethical practices in undertaking bioinformatics approaches in the course of healthcare. While dealing with patients’ genomic data, there is the need to consider different ethical practices. When it comes to the management of data in bioinformatics, ethical practices play critical roles in ensuring guidance to the operational processes. Ethical policies are necessary for ensuring that all the processes or the necessary tools and procedures are incorporated in the bioinformatics toolkit. Evidence-based ethical policies ought to be followed to ensure that all the bioinformatics tools are used appropriately for better outcomes. In most cases, policies are formulated to provide guidelines on different practices and the procedures that can be followed to ensure that all the requirements and integrated for better outcomes.

Guidelines Detailing How to Apply the Policy in Practice

Evidence-based ethical policies are applicable in guiding the processes and procedures in bioinformatics. The policy can be applied in the management of resources and the procedures required in bioinformatics. Bioinformatics involves the application of computational and analysis tools to gather and interpret biological or clinical data for the benefit of transforming the entire healthcare practice. Therefore, ethical practices need to be fully integrated to ensure better outcomes. Ethical policies formulated, and everybody involved in the bioinformatics processes should adhere to all the required practices. The policy can be applied to transform the perception of people and to enhance the ideas geared towards ensuring effective outcomes.

Practical Recommendations To Assist In Implementing the Use of Bioinformatics

The implementation of bioinformatics requires adherence to the set guidelines. The guidelines ought to be connected to the policies under consideration. In particular, the implementation of bioinformatics requires consideration of ethical practices given the use of data and information. Successful bioinformatics analysis needs to be based on the appropriate experimental design. These designs should start with effectively designed experimental approaches with a well-defined hypothesis and simple strategies to aid the understanding of the entire procedures (Chojnacki et al., 2017). While implementing bioinformatics, there is also the need to establish successfully executed experiments associated with attentive experimental designs. Finally, there is the need for collaboration and communication regarding possible pitfalls and limitations of the entire bioinformatics project, including resources, technology, as well as the processes of analysis. All these processes ought to be observed before undertaking the experiments.

How to How Educate Stakeholders on This New Practice

Education of stakeholders is essential in ensuring success in the implementation of the use of bioinformatics. Stakeholders should therefore be educated on different procedures that ought to be undertaken to realize the success of the entire process. Organizations should conduct training to ensure that all the stakeholders, particularly those directly involved in the implementation processes, are well aware of the entire procedures and processes. Stakeholders should be educated on the ethical and legal procedures of bioinformatics approaches. The educational processes should also be based on the effective management of data (Zheng et al., 2020). Some of the ethical practices to be observed in the educational processes include confidentiality of information, consent, and adherence to the quality procedures in ensuring positive outcomes.

When To Monitor Data to Evaluate Outcomes on the Use of the Policy

While undertaking bioinformatics, there is the need to consider the flow of data. These data should be monitored consistently in the course of the entire operation. However, the evaluation/analysis should be done at the end of the implementation processes to encourage full assessment of the entire bioinformatics process. While analyzing data, there is the need to start from the initial stages when the information was first recorded. The collection of original data will always give an honest insight into what should be done to adjust the bioinformatics procedures. The outcome of data analysis should be able to point out the areas of weaknesses and the possible pitfall in the entire project; this will enable the entire stakeholders to understand the areas that require possible adjustments.

Example of Bioinformatics

One of the specific examples of bioinformatics is the application of computer analysis on the human genome project. The project has resulted in over three billion basic pairing of human DNA components. Ethical policies, guidelines, as well as the recommendations stated above have resulted in quality outcomes in the analysis of the human genome. Further, observing these guidelines, policies, as well as recommendations will lead to greater innovations and improvements in the entire process of genome sequencing.

Conclusion

Bioinformatics approaches are necessary for the management of modern clinical biology and medicine. Bioinformatics often involves the application of a toolbox that has to be fully integrated with all the required components. Tool kit for implementing bioinformatics in an organization should incorporate different factors. In bioinformatics, ethical practices need to be fully integrated to ensure better outcomes. Ethical policies formulated, and everybody involved in the bioinformatics processes should adhere to all the required practices. Some of the ethical practices to be considered may include confidentiality of information, quality procedures are done in line with the set guidelines, and consent.

References

Baxevanis, A. D., Bader, G. D., & Wishart, D. S. (Eds.). (2020). Bioinformatics. John Wiley & Sons.

Chen, L., Heikkinen, L., Wang, C., Yang, Y., Sun, H., & Wong, G. (2019). Trends in the development of miRNA bioinformatics tools. Briefings in bioinformatics, 20(5), 1836-1852. https://doi.org/10.1093/bib/bby054

Chojnacki, S., Cowley, A., Lee, J., Foix, A., & Lopez, R. (2017). Programmatic access to bioinformatics tools from EMBL-EBI update: 2017. Nucleic acids research, 45(W1), W550-W553. https://doi.org/10.1093/nar/gkx273

Roumpeka, D. D., Wallace, R. J., Escalettes, F., Fotheringham, I., & Watson, M. (2017). A review of bioinformatics tools for bio-prospecting from metagenomic sequence data. Frontiers in genetics, 8, 23. https://doi.org/10.3389/fgene.2017.00023

Zheng, H., Zhang, G., Zhang, L., Wang, Q., Li, H., Han, Y., … & Guo, X. (2020). Comprehensive review of web servers and bioinformatics tools for cancer prognosis analysis. Frontiers in oncology, 10, 68. https://www.frontiersin.org/articles/10.3389/fonc.2020.00068/full

Appendix

Sample Data Genome Project Data

Index of /pub/release-105/fasta/homo_sapiens/dna/