ISSN 1476-4687, Salesforce Inc. (2021c) Slack. These formats allow encoding quantitative information about the variant, such as variant allele fraction, depth of coverage at the variant position, and genotype quality. J Comput Mediat Commun 12(2):712732, Zoom Video Communications Inc. (2020) Zoom for video, conferencing, and phones. In addition, in large groups the participants they sometimes perceived their collaborators as being apathetic or uninterested in the details of the project. The context menu can also enable easy linking to shared datasets. Such a user interface allows trained molecular pathologists and practitioners to interpret the clinical significance of the genetic alterations and release a comprehensive molecular report. This phenomenon is supported by our data in that 17 of our participants with different backgrounds, i.e., less common ground, encountered language barriers that inhibited collaboration by requiring extra effort to successfully discuss project goals and tasks. This is frequently manifested when lack of informal interactions led to doubts about their collaborators prioritization of the project, creating concern that a vital part of the project would not be completed. Int J Hum Comput Stud 60(3):365380, The National Research Council (2000) Addressing the nations changing needs for biomedical and behavioral scientists. We examine the communication and collaboration challenges in multidisciplinary research through an interview study with 20 life-science researchers. Readers should consult the references for additional details. We presented the results of semi-structured interviews that examined the challenges associated with collaborative life science research. In this case, the system should notify members of a task chain notifying them that the dependent task has been completed and the new tasks may now begin. Many disciplines, from human genetics and oncology to plant breeding, microbiology and virology, commonly face the challenge of analyzing rapidly increasing numbers of genomes. Source: Clinical Laboratory News. Identifying phased variants is one of the challenges. Variant nomenclature is an essential part of a clinical report and represents the fundamental element of a molecular test result. Authors David Eisenberg 1 , Edward Marcotte , Andrew D McLachlan , Matteo Pellegrini Affiliation This article will discuss some important practical considerations for laboratory directors and bioinformatics personnel when developing NGS-based bioinformatics resources for a clinical laboratory. Here, the authors present their opinions on what the main bioinformatic challenges are in transferring bacterial . Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of . AACC.org Our results show that involving various disciplines creates language barriers that delay life science projects. 113, Swigger K, Alpaslan F, Brazile R, Monticino M (2004) Effects of culture on computer-supported international collaborations. Detection of structural DNA variation from next generation sequencing data: A review of informatic approaches. This allows portability across different IT platforms in healthcare systems and the cloud and avoids software conflicts. In order to have high confidence in the performance of NGS results, laboratories must perform a thorough validation as described in practice guidelines (1). Springer, Balestrini M, Kotsev A, Ponti M, Schade S (2021) Collaboration matters: capacity building, up-scaling, spreading, and sustainability in citizen-generated data projects. This property of NGS data enables laboratories to identify a vast repertoire of genetic alterations from a single NGS run on a sample using different bioinformatics algorithms (4) (Figure 1). PLoS Comput Biol 10(11):e1003896, Google Inc. (2021a) Google docs. As stated in section Methods, all procedures performed in studies involving human participants were in accordance with the ethical standards of the institutional and with the 1964 Helsinki Declaration and its later amendments or comparable ethical standards. However, we found that the interdisciplinary nature of these projects cause technical language barriers and differences in methodology affect trust. However, the need to find expertize in an specific area often results in the creation of a team where trust has not been previously established. (2017) recently implemented a one-hour professional development course aimed at undergraduate students participating in the National Institute for Mathematical and Biological Synthesis Summer Research Experience that focused on developing collaboration skills. (2021) Towards complete and error-free genome assemblies of all vertebrate species. Standardisation of methods used in clinical practice (may very well be region and country-specific) Certification of who can call themselves a bioinformatician. Unlike virtual machines, containers are a lightweight Linux operating system process that isolates the software running inside the container from all other running applications on the computer. The multiple components of a bioinformatics pipeline frequently have dependencies on different software run-times and in some instances, different versions of the same software. Its usually because the people theyre like, first of all, we know them. Edge-case scenarios related to the nature of sequencing data or unexpected changes in the deployment environment can significantly, often silently, impact NGS test results. Participation in interviews was voluntary and participants did not receive compensation. Abstract The sequencing of the human genome has made it possible to identify an informative set of >1 million single nucleotide polymorphisms (SNPs) across the genome that can be used to carry out genome-wide association studies (GWASs). Building a robust bioinformatics infrastructure undeniably requires staff with expertise and training in bioinformatics and software engineering, strategic planning, and phased implementation, including validation and version control before clinical testing is performed. The sequence alignment process assigns a genome positional context to the short reads in the reference genome and generates several metadata fields, including alignment characteristics (matches, mismatches, and gaps) in Concise Idiosyncratic Gapped Alignment Report format. Front Genet 2019;10:426. A lot of the collaborations have addressed scientific questions that I would have otherwise not have been able to do with my skill set. Appropriate automation of bioinformatics resource development and deployment in clinical production contributes to optimized test turnaround time, better productivity of the bioinformatics team, and maintainable infrastructure (10,11). Roy S, Coldren C, Karunamurthy A, et al. Kadri S, Roy S. Platform-agnostic deployment of bioinformatics pipelines for clinical NGS assays using containers, infrastructure orchestration, and workflow manager (Abstract #I031). This work is partially supported by National Science Foundation Grant Award #IIS-2013998. Publishers note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. Morgan Kaufmann Publishers Inc., San Francisco, CA, USA, Bonde D (2013) Qualitative interviews: when enough is enough. J Manag Inform Syst 28(1):273310, Shapiro B (2017) Pathways to de-extinction: how close can we get to resurrection of an extinct species? We use these findings to guide our recommendations for technology to support life science. We found several instances of this additional work, particularly when coordinating meetings (especially across multiple time zones and in different languages) and ensuring that everyone is up-to-date with the project status. Int J Confl Manag 12(3):212238. Training programs should provide mechanisms for facilitating, simplifying, and documenting these conversations. For example, we envision a specialized word processor similar to Microsoft Word Online (Microsoft Inc., 2021b) or Google Docs (Google Inc., 2021a) that enable remote collaborators to collaboratively work on a document and easily import output of computational programs. Sarah Morrison-Smith,Catherine OBrien&Nazaret Cuadros, University of Florida, Gainesville, FL, USA, University of Minnesota, Minneapolis, MN, USA, You can also search for this author in In this paper . Challenge Problems in Bioinformatics and Computational Biology from . Life-science researchwhich encapsulates a wide range of biological and biomedical researchis responsible for many major scientific findings in the past decade. Moreover, the participants were more engaged and had higher perception of their colleagues work when they were knowledgeable of that proponent of the project. Humanit Soc Sci Commun 8(1):169, Article In: Proc. One of the first technologiesso called first generation sequencing technologieswas capable of sequencing a couple of thousand nucleotides of a DNA sample per day. This weblog post aims to highlight the importance and significance of device getting to know in bioinformatics, provide an outline of bioinformatics and gadget mastering, explore the . Data Science and Engineering 2017;2:245-51. ISSN 1047-7039, Hinds PJ, Mortensen M (2005) Understanding conflict in geographically distributed teams: the moderating effects of shared identity, shared context, and spontaneous communication. A sophisticated software application that is deployed using several containers is typically managed in a production environment using container orchestration platforms such as Kubernetes, Mesos, Docker Swarm, and cloud vendor-specific frameworks. The most critical requirement for implementing a bioinformatics pipeline is a proper, systematic clinical validation in the context of the entire next-generation sequencing (NGS) assay (1,12). After the experiment, the biological material (DNA or RNA) is extracted from the organisms using laboratory methods. Interestingly, we found instances where the work culture shifted from collaborative to competitivenamely when interdisciplinary teams increased expertize in a specific area, this frequently lead to territorial issues. In this congress, a variety of research . pp. Comput Struct Biotechnol 18:919, Article 379, Mangul S, Martin LS, Hoffmann A, Pellegrini M, Eskin E (2017) Addressing the digital divide in contemporary biology: lessons from teaching UNIX. (2019) Large-scale transdisciplinary collaboration for adaptation research: Challenges and insights. In the process, they recommended that transdisciplinary training strengthen individuals communication skills that build and sustain cooperation among team members, management strategies for resolving interpersonal conflict, and foster the ability to reach a consensus regarding research goals and visions to reduce task-related uncertainty. Consequently, for clinical testing, accidentally missing a BED file due to inconsistent transfer from development to the production environment may produce false-negative results and significantly impact patient care. To avoid these issues researchers often constrain teams to their current network of collaborators and when forced to reach out rely on the collaborators of trusted collaborators. The system would also allow researchers to view and visualize (when appropriate) all results of a pipeline to enable comparisons between pipeline executions and datasets. Our results show that both interdisciplinarity and differences in work culture and practices affect collaboration in life science. In Proc. Table of Contents show Laboratories should determine a pipelines performance characteristics based on the types of variants the NGS test intends to detect and should consider the sample matrix, such as fresh tissue, peripheral blood, or formalin-fixed paraffin-embedded tissue. Thus, one recommendation that stems from our findings is to have training programs of varied sizes and disciplines; smaller discussion sections or research project groups will allow further engagement and understanding into the scientific progress. SN Appl Sci 2(6):1096, Morrison-Smith S, Boucher C, Bunt A, Ruiz J (2015) Elucidating the role and use of bioinformatics software in life science research. Temporal complexity and coding. (2001) The sequence of the human genome. Ensuring consistent, on-demand access to these resources presents several challenges in clinical laboratories. https://zoom.us/. (P3). Participants frequently stated that mutual respect and trust were necessary for project engagement and success. Together, these the proposed features would enable a shared sense of ownership of the project while also providing a better sense of each members progress toward the shared goals. Wiley Publishing, Luikart G, Kardos M, Hand BK, Rajora OP, Aitken SN, Hohenlohe PA (2018) Population genomics: advancing understanding of nature. We recruited participants via science discussions on Reddit (Reddit.com, 2017) and email. To make learning bioinformatics fun and easy, we have founded Rosalind, a platform for learning bioinformatics through problem solving. population genomics. 900 Seventh Street, NW Suite 400 If material is not included in the articles Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. In the case of next generation sequencing, the signal produced is fluorescent light that can be viewed under a microscope that can be translated into a nucleotide (A, C, G, or T) sequence, and in the case of mass spectrometer there is ion/mass charge that is interpreted to produce an amino acid sequence corresponding to a peptide. In contrast to traditional Sanger sequencing, with read lengths of 500-900 base pairs (bp), short reads of NGS range in size from 75 to 300 bp depending on the application and sequencing chemistry. The questions above are a small sample of those that face our nascent field as we enter a new century. Sometimes, and almost inevitably put publication of the research in jeopardy. Nature 592(7856):737746. Sage Publications, Sturner KK, Bishop P, Lenhart SM (2017) Developing collaboration skills in team undergraduate research experiences. The authors review advances in ensemble deep learning methods and their applications in bioinformatics, and discuss the challenges and opportunities going forward. Collaboration has been extensively studied over the past several decades from a variety of perspectives including the sciences (Armenteras, 2021; Olson and Olson, 2000, 2006) and the humanities (Balestrini et al., 2021; Canfield, 2020; Cooke et al., 2017). And some of those projects, well they may have been completed, but theyve never been published. https://slack.com, Sarker S, Ahuja M, Sarker S, Kirkeby S (2011) The role of communication and trust in global virtual teams: a social network perspective. Bacterial whole-genome sequencing is showing promise in clinical applications. If you know the answer to this question it will be much. This fluctuation in interest levels has important implications for design of training programs to ensure the engagement of the trainees. Detection, accurate representation, and the nomenclature of sequence variants can be challenging depending upon the variant type, sequence context, and other factors. GigaScience 7(6):giy061, Article 5(9):11931194, Armstrong DJ, Cole P (2002) Managing distances and differences in geographically distributed work groups. The integration of the pipeline with other software systems can also be challenging. Principles and recommendations for standardizing the use of the next-generation sequencing variant file in clinical settings. Several aspects of the pipeline can impact performance characteristics and affect the sensitivity of variant detection. One study compared output from the AI chatbot for medical questions with answers from physicians 1; other studies have evaluated the AI chatbot's responses to sample clinical vignettes. Nature 585:7984, Article Data analysis frequently consists of some combination of bioinformatics and statistics, and may result in scientific conclusions or suggestions for follow-up studies. While Walsh and Maloney (2007) asserted that remote collaborations do not experience more challenges associated with culture than co-located teams, results from our study demonstrate that differences in work culture, particularly work practices regarding methodology and data sharing, profoundly affect collaboration in life science. Hsi-Yang Fritz M, Leinonen R, Cochrane G, et al. This is appropriate for semi-structured interviews as qualitative coding results in the possibility of applying the same code to different sections of the interview (Jun et al., 2018). Bioinformatic challenges for the next decade (s) Philos Trans R Soc Lond B Biol Sci. However, further research is required to identify methods for training these skills in a manner that prepares students for life science research. of a conference sponsored by the American Cancer Society, the Burroughs Wellcome Fund, and the Howard Hughes Medical Institute, Cooke SJ, Gallagher AJ, Sopinka NM, Nguyen VM, Skubel RA, Hammerschlag N, Boon S, Young N, Danylchuk AJ (2017) Considerations for effective science communication. This technology was fundamental to the sequencing and assembly of the first human genome (International Human Genome Sequencing Consortium, 2001; Venter, 2001). This makes it crucial that labs understand and evaluate the region of the genome sequenced by the NGS assay for accurate clinical reporting. In addition, a split-read alignment strategy identifies gene fusions from genomic DNA sequencing (7). All of these technologies have been dramatically advanced over the past couple decades, and other laboratory methods (such as optical mapping (Mukherjee, 2018)) have been automated (Giani et al., 2020). There have been many barriers to purchasing and implementing the new wave of software on the market today . Google Scholar, Battin RD, Crocker R, Kreidler J, Subramanian K (2001) Leveraging resources in global software development. Thus, the question of how to prepare trainees for collaboration in life science research remains open. Biological and biomedical research is increasingly conducted in large, interdisciplinary collaborations to address problems with significant societal impact, such as reducing antibiotic resistance, identifying disease sub-types, and identifying genes that control for drought tolerance in plants. Cummings and Kiesler (Cummings and Kiesler, 2005) work found that projects incorporating multiple disciplines had as many positive outcomes as projects involving fewer. Plant biology: understanding and mitigating the physiological, genetic and biological effects of environmental stressors on plants. PubMed Researchers are frequently involved with multiple scientific projects, and, thus, they prioritize their efforts. Background Modeling of single cell RNA-sequencing (scRNA-seq) data remains challenging due to a high percentage of zeros and data heterogeneity, so improved modeling has strong potential to benefit many downstream data analyses. We recruited several participants (P1-9) from an existing collaborative project; whereas the remaining were independent of each other. Clinical Laboratory News Seeking Answers from Big Data in the Era of Precision Medicine Cancer data can be fragmented and compartmentalized, and many stakeholders are trying to overcome the challenges this poses for advancing research forward. A clinical laboratory, with the assistance of a bioinformatics professional or team, reviews, understands, and documents each component of the pipeline, the data dependencies, input/output constraints, and develops mechanisms to alert for unexpected errors. Our participants, such as P3, expressed that the addition of collaborators in a project can pose challenges if the expertize overlaps because there is potential for territorial actions that foster animosity and jeopardize the projects success (e.g., competition for funding sources): Because you are working in the same field and you are doing the same stuff, there is more potential for territorial actions versus when you are working with people totally outside, they have their own funding sources. You have to speak in terms of their language. These findings are compounded by prior work showing that the development of communication technology has negatively impacted projects by hindering information sharing (Hinds and Mortensen, 2005), delaying outcomes (Espinosa, 2004), and causing misunderstandings (Cramton, 2001). First I do what I can do on my side and then try to make everything easier and convenient for my collaborators (P18). +Email: [emailprotected]. Subsequent updates to the bio-informatics pipeline should undergo appropriate revalidation and systematic version control (See Box p. 16). Oct 24, 2021 Genomics and Bioinformatics: Challenges and Opportunities Lilit Nersisyan Illustration by Armine Shahbazyan. Our participants felt that although they may not need to actively participate in all aspects of the project, they would be more engaged if they had knowledge of each proponent of the scientific process. The ability to identify and analyze health trends, and build the treatments of the future using AI and bioinformatics is a skillset that will only grow in importance and necessity in years to come. Unlike in qualitative coding, however, instead of each researcher independently organizing data followed by calculating the groups inter-rater reliability, a quantitative measure, the five researchers analyzing the data came to a consensus on all responses. Hence, this sense of project involvement is particularly important when researchers are concerned that improper prioritization jeopardizes the projects timeline. PubMed Central HUB brought together around 40 bioinformaticians from academia and industry to discuss the 'Biggest Challenges in Bioinformatics' in a 'World Caf' style event. These key findings demonstrate that collaboration challenges are still impacting life science, despite years of collaboration research. Sometimes its taking something that is complicated and explaining so its understandable. Currently, the task of interpreting genetic data is exclusively in the domain of clinical and . I have limited abilities, there are some things I know how to do and a bunch of things I dont. Am J Prevent Med 35(2):S133S140, Olson GM, Olson JS (2000) Distance matters. The result is that the ability to determine DNA sequences is starting to outrun the ability of researchers to store, transmit and especially to analyze the data. Prior research (Morrison-Smith et al., 2015) showed that in order to overcome the challenges of analyzing data, life science researchers collaborate with researchers and trainees in different disciplines, locations, and institutions. This indicates that there is a clear need to further investigate the collaboration challenges faced by life science researchers. This past spring, they finally had the chance to see the game in action. Genome Res 2011;21:734-40. Computational biology and bioinformatics is an interdisciplinary field that develops and applies computational methods to analyse large collections of biological data, such as genetic sequences,. Kevin. Yet earlier research on interdisciplinary science showed that scientific projects that depend on a large number of institutions and disciplines are less successful than those relying on fewer (Cummings and Kiesler, 2005; Kiesler and Cummings, 2002); here, success was defined to include metrics such as graduate and post-graduate supervision, the number of related projects, the frequency of project meetings, and the likelihood of having created a project-related course. While prior work has examined the challenges resulting from differences in project-related terminology (Morrison-Smith et al., 2015). Recently available high throughput multi-omics data may offer a great opportunity to explore the underlying mechanisms of diseases and improve disease heterogeneity assessment throughout the treatment course. Although software has been developed to assist in creating and running data analysis pipelines (e.g., Galaxy (Afgan et al., 2018)), there is a need for a project management system explicitly tailored to life science pipelines and life science project workflows. Pharmacogenomics requires the integration and analysis of genomic, molecular, cellular, and clinical data, and it thus offers a remarkable set of challenges to biomedical informatics. Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. Wang X, Liotta L. Clinical bioinformatics: A new emerging science. In the meantime, to ensure continued support, we are displaying the site without styles In: Proc of European Software Process Improvement (Euro SPI), Cech TR, Bond EC, Stevens J (2000) The role of the private sector in training the next generation of biomedical scientists. It is essential that the pipeline validation include such interface functions. Clinical molecular laboratories performing NGS-based assays have as an implementation choice one or more bioinformatics pipelines, either custom-developed by the laboratory or provided by the sequencing platform or a third-party vendor. In 2008, Stokols et al. Biochem Mol Biol Educ 47(3):288295, Maynard MT, Gilson LL (2014) The role of shared mental model development in understanding virtual team effectiveness. 2006 Mar 29;361 (1467):525-7. doi: 10.1098/rstb.2005.1797. We interviewed local participants at their primary workspace (office or lab), and interviewed the remaining participants via Skype or over the phone. It can be really hard to tell where they put our collaboration project into priority, but you can tell from email commentsometimes you can tell theyre working and I get email back really soon, but sometimes its like after a couple of weeks may be months then I get a response. For example, a data analysis pipeline can be set up such that when new datasets are added to the shared project, the pipeline is automatically run with the new dataset and the results are stored and shared. In some projects, experiments cannot be redone, in which case the participants felt they must reformat the data or work with what [they] get" (P7). CAS The authors declare no competing interests. Automation helps manage bioinformatics resources and workflows and streamlines day-to-day bioinformatics operations. The curriculum for these certificate programs could include formal pedagogy from the team science research literature, as well as experiential activities. During the validation and implementation of bioinformatics resources in a clinical laboratory, it is crucial to ensure compliance with Federal, state and local regulations as well as specific accreditation requirements (e.g. A review of bioinformatic pipeline frameworks. ". Nowhere is this challenge more evident than in oncology, as much of these data will come from studies of patients with cancer. Estimating a pipelines false-negative rate accurately can be challenging. It can be argued that the seminal 1953 article by Watson and Crick ( Watson and Crick, 1953) is in fact a modeling paper and arguably the first structural bioinformatics paper.Thus, the 2014 Nobel prize for 'multiscale modeling' to Martin Karplus, Arie . In: Converging disciplines. Here, we summarize our main findings that largely stem from the interdisciplinary nature of the projects. The total number of reads from the sample that align to one of the known fusion sequences can be counted to identify and quantify the gene fusion (Figure 1) (8). J Mol Diagn 2019;21:384-9. In a worst-case scenario, improper technique can make the data unusable: Shes probably spent 50 to 100 thousand dollars on sequencing and has nothing to show for it simply because proper controls werent done. We also present recommendations for life science research training programs and note the necessity for incorporating training in project management, multiple language, and discipline culture. Therefore, oneperhaps most obviousfinding of our work is need for life science training programs to be multidisciplinary. Motivation: Widespread availability of low-cost, full genome sequencing will introduce new challenges for bioinformatics. In light of this focus, we conducted semi-structured interviews with life science researchers from nine research institutions. The resulting data are then transferred to the participants computer or server and analyzed. New methods are needed in four areas to realize the potential of . Last year, Marcel Duvivier, Jeremiah Mubiru and Ana Perez Cespedes started developing a video game to help kindergarten through ninth grade students in the David's Challenge program learn addition, subtraction, multiplication and division.
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