Bioinformatics meets user-centred design: a perspective

Designers have a saying that "the joy of an early release lasts but a short time. The bitterness of an unusable system lasts for years." It is indeed disappointing to discover that your data resources are not being used to their full potential. Not only have you invested your time, effort, and research grant on the project, but you may face costly redesigns if you want to improve the system later. This scenario would be less likely if the product was designed to provide users with exactly what they need, so that it is fit for purpose before its launch. We work at EMBL-European Bioinformatics Institute (EMBL-EBI), and we consult extensively with life science researchers to find out what they need from biological data resources. We have found that although users believe that the bioinformatics community is providing accurate and valuable data, they often find the interfaces to these resources tricky to use and navigate. We believe that if you can find out what your users want even before you create the first mock-up of a system, the final product will provide a better user experience. This would encourage more people to use the resource and they would have greater access to the data, which could ultimately lead to more scientific discoveries. In this paper, we explore the need for a user-centred design (UCD) strategy when designing bioinformatics resources and illustrate this with examples from our work at EMBL-EBI. Our aim is to introduce the reader to how selected UCD techniques may be successfully applied to software design for bioinformatics.     

A Distributed Multi-Storage Resource Architecture and I/O Performance Prediction for Scientific Computing

I/O intensive applications have posed great challenges to computational scientists. A major problem of these applications is that users have to sacrifice performance requirements in order to satisfy storage capacity requirements in a conventional computing environment. Further performance improvement is impeded by the physical nature of these storage media even when state-of-the-art I/O optimizations are employed.In this paper, we present a distributed multi-storage resource architecture, which can satisfy both performance and capacity requirements by employing multiple storage resources. Compared to a traditional single storage resource architecture, our architecture provides a more flexible and reliable computing environment. This architecture can bring new opportunities for high performance computing as well as inherit state-of-the-art I/O optimization approaches that have already been developed. It provides application users with high-performance storage access even when they do not have the availability of a single large local storage archive at their disposal. We also develop an Application Programming Interface (API) that provides transparent management and access to various storage resources in our computing environment. Since I/O usually dominates the performance in I/O intensive applications, we establish an I/O performance prediction mechanism which consists of a performance database and a prediction algorithm to help users better evaluate and schedule their applications. A tool is also developed to help users automatically generate performance data stored in databases. The experiments show that our multi-storage resource architecture is a promising platform for high performance distributed computing.     

ddrage: A data set generator to evaluate ddRADseq analysis software

High‐throughput sequencing makes it possible to evaluate thousands of genetic markers across genomes and populations. Reduced‐representation sequencing approaches, like double‐digest restriction site‐associated DNA sequencing (ddRADseq), are frequently applied to screen for genetic variation. In particular in nonmodel organisms where whole‐genome sequencing is not yet feasible, ddRADseq has become popular as it allows genomewide assessment of variation patterns even in the absence of other genomic resources. However, while many tools are available for the analysis of ddRADseq data, few options exist to simulate ddRADseq data in order to evaluate the accuracy of downstream tools. The available tools either focus on the optimization of ddRAD experiment design or do not provide the information necessary for a detailed evaluation of different ddRAD analysis tools. For this task, a ground truth, that is, the underlying information of all effects in the data set, is required. Therefore, we here present ddrage , the ddRA D Data Set Ge nerator, that allows both developers and users to evaluate their ddRAD analysis software. ddrage allows the user to adjust many parameters such as coverage and rates of mutations, sequencing errors or allelic dropouts, in order to generate a realistic simulated ddRADseq data set for given experimental scenarios and organisms. The simulated reads can be easily processed with available analysis software such as stacks or pyrad and evaluated against the underlying parameters used to generate the data to gauge the impact of different parameter values used during downstream data processing.     

Use of online resources in the taxonomy and ecology of harmful phytoplankton

The internet is becoming increasingly important for the dissemination of biological information. Large target audiences are reached rapidly, large amounts of information can be assembled and distributed, sites can include search facilities, and information might be handled online or as printable output. Many websites are now producing libraries of phytoplankton images including toxic dinoflagellates. But while some provide valuable resources others lack focus and do not address any specific problems, for example the morphological variability in many major groups such as Dinophysis and Alexandrium. Yet it is this morphological variation which often hinders taxonomic and ecologic research of harmful dinoflagellates. Taxonomic information as well as information about sample origin and preservation methods is also often lacking. This makes comparisons between taxonomic websites difficult. Therefore, while documenting the presence of certain taxa, some sites cannot be used as a taxonomic training or research tool. Yet, if online resources were to reflect these complexities they could become valuable tools in the dissemination of data as well as actual research and training tools. One reason for the lack of consistency between sites could be that these sites, as a teaching and research tool, are a relatively recent development and no criteria have therefore been established as to the contents and structure of such sites, as are commonplace for conventional publications. This comment will discuss different approaches to, and tools for, the production of online taxonomic resources (depending on the site's objectives, e.g. research or teaching) using the Harmful Plankton Project ( http://www.liv.ac.uk/hab ) designed at the University of Liverpool as one example of a user‐friendly and adaptable tool.     

GP registrars as teachers: a survey of their level of involvement and training

The role of general practice in medical education is increasing both at the undergraduate and postgraduate level. There is a paucity of evidence as to the level of involvement of GP registrars and their training to teach. Two hundred and forty one GP trainees in the Peninsula Deanery were surveyed as to their current level of involvement in teaching and their training to provide it. Seventy eight completed surveys were returned and these revealed that 62% were regularly involved in teaching but only 41% had ever received any training in this area. There was a strong feeling that teaching was an important skill for GPs with 92% of trainees wanting further training in this area. There is clearly a need for further research in this area both to identity whether this sample is representative of the situation nationally and to determine how best to equip trainees in their roles as educators now and in the future.     

What do Wessex general practitioners think about the structure of hospital vocational training?

OBJECTIVES--To assess the views of general practitioners about the structure and content of hospital vocational training and its relation to the training year. DESIGN--Postal questionnaire. SETTING--Wessex, England. SUBJECTS--General practitioner trainees undertaking practice training year (n = 144), course organisers (n = 22), and a random sample of two thirds of trainers (n = 135). RESULTS--Questionnaires were returned from 86% (260): 84% of trainees (121), 92% of trainers (124), and 68% of course organisers (15). Most respondents in all groups (84.3%, 95% confidence interval 79.7% to 88.8%) wanted more jobs lasting two and three months to allow a greater range of hospital specialties to be experienced and some of the training year to be carried out before hospital jobs (66.3%, 60.4% to 72.1%). Most hospital specialties were rated at least 6 out of 10 as "useful" for general practice training. A substantial minority of training posts did not have regular weekly teaching (166/541; 30.7%, 26.8% to 34.6%) and had no half day (224/541; 41.4%, 37.3% to 45.6%), and over half gave no study leave (293/541; 54.2%, 50.0% to 58.4%). CONCLUSIONS--The structure of hospital training should be reviewed as it does not reflect the views of most trainees, course organisers, or trainers. Individual posts need closer supervision to ensure the availability of basic training requirements. More trainees should be allowed to spend a short time in the general practice before hospital rotations and to choose a greater range of shorter jobs.     

E-learning助推临床微生物教学数字化转型

由于医学知识的快速增加、新病原体的出现、新传染病的产生和新耐药机制的形成,在临床微生物学领域具有学习和应用能力并不断提升是一项不容忽视的挑战。E-learning是一种教学方法,它基于使用电子媒体和设备作为工具,以改善获得培训、交流和互动的机会,并促进学生适应新的知识和技能。在临床微生物学教学和培训中E-learning可以提供更高效灵活的模式来满足教育需求。E-learning为教育工作者提供了新的角色,在数字技术的帮助下设计和促进更好的学习体验,引导学生正确掌握临床微生物学的电子资源,促进了理论和实践差距的缩小。作为一种E-learning的新方法,虚拟实验室通过重新激活和场景模拟提供了更广泛有效的学习平台。多平台整合教育资源,让学生更容易理解和掌握日新月异的医学知识,促进临床微生物教学观念转换、数字化转型和教学模式改革。

     

Hospital training for general practice: views of trainees in the North Western region.

Vocational trainees in the North Western region who were in their general practice year completed a questionnaire concerning the hospital component of their training. Replies were received from 125 trainees, providing information about 451 hospital posts. In a total of 372 posts (85%) less than two hours of formal teaching a week was provided. Trainees stated that they received no informal teaching in nearly one third of posts. The orientation of teaching towards general practice was reported as greatest in the posts that were not part of a vocational training scheme. Study leave was applied for by doctors in only 163 (37%) posts, usually to prepare for or to sit an examination. There seem to be serious educational deficiencies in hospital posts that are used to train both general practitioners and other specialists. Improvements in both the quantity and quality of in service teaching are therefore needed urgently.     

A Toolkit for ARB to Integrate Custom Databases and Externally Built Phylogenies

Researchers are perpetually amassing biological sequence data. The computational approaches employed by ecologists for organizing this data (e.g. alignment, phylogeny, etc.) typically scale nonlinearly in execution time with the size of the dataset. This often serves as a bottleneck for processing experimental data since many molecular studies are characterized by massive datasets. To keep up with experimental data demands, ecologists are forced to choose between continually upgrading expensive in-house computer hardware or outsourcing the most demanding computations to the cloud. Outsourcing is attractive since it is the least expensive option, but does not necessarily allow direct user interaction with the data for exploratory analysis. Desktop analytical tools such as ARB are indispensable for this purpose, but they do not necessarily offer a convenient solution for the coordination and integration of datasets between local and outsourced destinations. Therefore, researchers are currently left with an undesirable tradeoff between computational throughput and analytical capability. To mitigate this tradeoff we introduce a software package to leverage the utility of the interactive exploratory tools offered by ARB with the computational throughput of cloud-based resources. Our pipeline serves as middleware between the desktop and the cloud allowing researchers to form local custom databases containing sequences and metadata from multiple resources and a method for linking data outsourced for computation back to the local database. A tutorial implementation of the toolkit is provided in the supporting information, S1 Tutorial. Availability: http://www.ece.drexel.edu/gailr/EESI/tutorial.php.     

Using Inverse Probability Bootstrap Sampling to Eliminate Sample Induced Bias in Model Based Analysis of Unequal Probability Samples

In ecology, as in other research fields, efficient sampling for population estimation often drives sample designs toward unequal probability sampling, such as in stratified sampling. Design based statistical analysis tools are appropriate for seamless integration of sample design into the statistical analysis. However, it is also common and necessary, after a sampling design has been implemented, to use datasets to address questions that, in many cases, were not considered during the sampling design phase. Questions may arise requiring the use of model based statistical tools such as multiple regression, quantile regression, or regression tree analysis. However, such model based tools may require, for ensuring unbiased estimation, data from simple random samples, which can be problematic when analyzing data from unequal probability designs. Despite numerous method specific tools available to properly account for sampling design, too often in the analysis of ecological data, sample design is ignored and consequences are not properly considered. We demonstrate here that violation of this assumption can lead to biased parameter estimates in ecological research. In addition, to the set of tools available for researchers to properly account for sampling design in model based analysis, we introduce inverse probability bootstrapping (IPB). Inverse probability bootstrapping is an easily implemented method for obtaining equal probability re-samples from a probability sample, from which unbiased model based estimates can be made. We demonstrate the potential for bias in model-based analyses that ignore sample inclusion probabilities, and the effectiveness of IPB sampling in eliminating this bias, using both simulated and actual ecological data. For illustration, we considered three model based analysis tools—linear regression, quantile regression, and boosted regression tree analysis. In all models, using both simulated and actual ecological data, we found inferences to be biased, sometimes severely, when sample inclusion probabilities were ignored, while IPB sampling effectively produced unbiased parameter estimates.     

Biological Databases for Hematology Research

With the advances of genome-wide sequencing technologies and bioinformatics approaches, a large number of datasets of normal and malignant erythropoiesis have been gener-ated and made public to researchers around the world. Collection and integration of these datasets greatly facilitate basic research and clinical diagnosis and treatment of blood disorders. Here we provide a brief introduction of the most popular omics data resources of normal and malignant hematopoiesis, including some integrated web tools, to help users get better equipped to perform common analyses. We hope this review will promote the awareness and facilitate the usage of public database resources in the hematology research.     

Impact of gender on the formation and outcome of formal mentoring relationships in the life sciences

Despite increasing representation in graduate training programs, a disproportionate number of women leave academic research without obtaining an independent position that enables them to train the next generation of academic researchers. To understand factors underlying this trend, we analyzed formal PhD and postdoctoral mentoring relationships in the life sciences during the years 2000 to 2020. Student and mentor gender are both associated with differences in rates of student’s continuation to positions that allow formal academic mentorship. Although trainees of women mentors are less likely to take on positions as academic mentors than trainees of men mentors, this effect is reduced substantially after controlling for several measurements of mentor status. Thus, the effect of mentor gender can be explained at least partially by gender disparities in social and financial resources available to mentors. Because trainees and mentors tend to be of the same gender, this association between mentor gender and academic continuation disproportionately impacts women trainees. On average, gender homophily in graduate training is unrelated to mentor status. A notable exception to this trend is the special case of scientists having been granted an outstanding distinction, evidenced by membership in the National Academy of Sciences, being a grantee of the Howard Hughes Medical Institute, or having been awarded the Nobel Prize. This group of mentors trains men graduate students at higher rates than their most successful colleagues. These results suggest that, in addition to other factors that limit career choices for women trainees, gender inequities in mentors’ access to resources and prestige contribute to women’s attrition from independent research positions.

Does the gender of academic mentors impact the careers of their trainees? In the life sciences, graduate and postdoctoral trainees of women mentors are less likely to continue on to positions as academic mentors than trainees of men. This study finds that gender inequality in mentors’ access to resources contributes to this disparity.     

Strategies for the reduction of live animal use in microsurgical training and education

Education and training in microsurgical techniques have historically relied on the use of live animal models. Due to an increase in the numbers of microsurgical operations in recent times, the number of trainees in this highly-specialised surgical field has continued to grow. However, strict legislation, greater public awareness, and an increasing sensitivity toward the ethical aspects of scientific research and medical education, emphatically demand a significant reduction in the numbers of animals used in surgical and academic education. Hence, a growing number of articles are reporting on the use of alternatives to live animals in microsurgical education and training. In this review, we report on the current trends in the development and use of microsurgical training models, and on their potential to reduce the number of live animals used for this purpose. We also share our experiences in this field, resulting from our performance of numerous microsurgical courses each year, over more than ten years. The porcine heart, in microvascular surgery training, and the fresh chicken leg, in microneurosurgical and microvascular surgery training, are excellent models for the teaching of basic techniques to the microsurgical novice. Depending on the selected level of expertise of the trainee, these alternative models are capable of reducing the numbers of live animals used by 80-100%. For an even more enhanced, "closer-to-real-life" scenario, these non-animated vessels can be perfused by a pulsatile pump. Thus, it is currently possible to provide excellent and in-depth training in microsurgical techniques, even when the number of live animals used is reduced to a minimum. With these new and innovative techniques, trainees are able to learn and prepare themselves for the clinical situation, with the sacrifice of considerably fewer laboratory animals than would have occurred previously.     

Yabi: An online research environment for grid,high performance and cloud computing

Background  

There is a significant demand for creating pipelines or workflows in the life science discipline that chain a number of discrete compute and data intensive analysis tasks into sophisticated analysis procedures. This need has led to the development of general as well as domain-specific workflow environments that are either complex desktop applications or Internet-based applications. Complexities can arise when configuring these applications in heterogeneous compute and storage environments if the execution and data access models are not designed appropriately. These complexities manifest themselves through limited access to available HPC resources, significant overhead required to configure tools and inability for users to simply manage files across heterogenous HPC storage infrastructure.     

A survey of Canadian rheumatology training programs, 1968 to 1978.

The committee on manpower of the Canadian Rheumatism Association retrospectively surveyed Canadian rheumatology training programs for the period 1968 to 1978. There were 133 trainees during that period, who accounted for a total of 201 trainee-years. Most trainee-years were taken up by first-year trainees, especially in the first half of the decade under study. Although three training centres accounted for two thirds of all the trainee-years, there was a progressive increase in the proportion of trainees attending other centres. The majority of trainees were Canadian medical graduates. More than one third of the alumni of these programs held full-time academic positions, and more than three quarters had some academic affiliation. One third were spending at least half of their professional time in teaching and research, but only 71 were spending half or more of their practice time in rheumatology in Canada. The remainder had established residence abroad or were spending at least half of their practice time in areas other than rheumatology. The rapid expansion of Canadian training programs has not been paralleled by a proportionate increase in rheumatologic manpower in Canada.     

Genetic algorithm based two-mode clustering of metabolomics data

Metabolomics and other omics tools are generally characterized by large data sets with many variables obtained under different environmental conditions. Clustering methods and more specifically two-mode clustering methods are excellent tools for analyzing this type of data. Two-mode clustering methods allow for analysis of the behavior of subsets of metabolites under different experimental conditions. In addition, the results are easily visualized. In this paper we introduce a two-mode clustering method based on a genetic algorithm that uses a criterion that searches for homogeneous clusters. Furthermore we introduce a cluster stability criterion to validate the clusters and we provide an extended knee plot to select the optimal number of clusters in both experimental and metabolite modes. The genetic algorithm-based two-mode clustering gave biological relevant results when it was applied to two real life metabolomics data sets. It was, for instance, able to identify a catabolic pathway for growth on several of the carbon sources. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users. J. A. Hageman and R. A. van den Berg contributed equally to this paper.     

Are the recommendations being met in the general practice year of vocational training? Trainees' views in the West Midlands region.

Vocational trainees in the West Midlands who were in their general practice year were sent a postal questionnaire to find out whether there were important differences between the criteria for training of the 1986 West Midland postgraduate education committee (based on national recommendations) and the perceptions of the trainees of their current trainers and practices. The response rate was 86.2% (75 out of 87). Sixty four per cent (48) of trainees reported that they received on average less than the recommended minimum of three hours of teaching time a week. They felt that experience was inadequate in paediatric surveillance (62.7%) and preventive medical care (37.3%). Most trainers gave topic teaching (90.7%), and few used role play (5%). Most of the trainees (52%) had not signed a contract, a third did not get help with recommended allowances, and 37% thought that their progress had not been reviewed. Several trainees commented on the excellence of their training practices, and most of the practices appeared to be keeping to the spirit of the recommendations. There are, however, discrepancies between what some trainees feel they receive and what is recommended.     

Data-dependent visualization of biological networks in the web-browser with NDExEdit

Networks are a common methodology used to capture increasingly complex associations between biological entities. They serve as a resource of biological knowledge for bioinformatics analyses, and also comprise the subsequent results. However, the interpretation of biological networks is challenging and requires suitable visualizations dependent on the contained information. The most prominent software in the field for the visualization of biological networks is Cytoscape, a desktop modeling environment also including many features for analysis.A further challenge when working with networks is their distribution. Within a typical collaborative workflow, even slight changes of the network data force one to repeat the visualization step as well. Also, just minor adjustments to the visual representation not only need the networks to be transferred back and forth. Collaboration on the same resources requires specific infrastructure to avoid redundancies, or worse, the corruption of the data. A well-established solution is provided by the NDEx platform where users can upload a network, share it with selected colleagues or make it publicly available.NDExEdit is a web-based application where simple changes can be made to biological networks within the browser, and which does not require installation. With our tool, plain networks can be enhanced easily for further usage in presentations and publications. Since the network data is only stored locally within the web browser, users can edit their private networks without concerns of unintentional publication. The web tool is designed to conform to the Cytoscape Exchange (CX) format as a data model, which is used for the data transmission by both tools, Cytoscape and NDEx. Therefore the modified network can be directly exported to the NDEx platform or saved as a compatible CX file, additionally to standard image formats like PNG and JPEG.     

Supporting tool suite for production proteomics

SUMMARY: The large amount of data produced by proteomics experiments requires effective bioinformatics tools for the integration of data management and data analysis. Here we introduce a suite of tools developed at Vanderbilt University to support production proteomics. We present the Backup Utility Service tool for automated instrument file backup and the ScanSifter tool for data conversion. We also describe a queuing system to coordinate identification pipelines and the File Collector tool for batch copying analytical results. These tools are individually useful but collectively reinforce each other. They are particularly valuable for proteomics core facilities or research institutions that need to manage multiple mass spectrometers. With minor changes, they could support other types of biomolecular resource facilities.