Post ‘omic’ era has resulted in the development of many primary, secondary and derived databases. Many analytical and
visualization bioinformatics tools have been developed to manage and analyze the data available through large sequencing
projects. Availability of heterogeneous databases and tools make it difficult for researchers to access information from varied
sources and run different bioinformatics tools to get desired analysis done. Building integrated bioinformatics platforms is one of
the most challenging tasks that bioinformatics community is facing. Integration of various databases, tools and algorithm is a
challenging problem to deal with. This article describes the bioinformatics analysis workflow management systems that are
developed in the area of gene sequence analysis and phylogeny. This article will be useful for biotechnologists, molecular
biologists, computer scientists and statisticians engaged in computational biology and bioinformatics research.
Analysis; bioinformatics; databases; phylogeny; integration; workflows
Objectives: The paper gives examples of the bioinformatics services provided in a variety of different libraries by librarians with a broad range of educational background and training.
Methods: Two investigators sent an email inquiry to attendees of the “National Center for Biotechnology Information's (NCBI) Introduction to Molecular Biology Information Resources” or “NCBI Advanced Workshop for Bioinformatics Information Specialists (NAWBIS)” courses. The thirty-five-item questionnaire addressed areas such as educational background, library setting, types and numbers of users served, and bioinformatics training and support services provided. Answers were compiled into program vignettes.
Discussion: The bioinformatics support services addressed in the paper are based in libraries with academic and clinical settings. Services have been established through different means: in collaboration with biology faculty as part of formal courses, through teaching workshops in the library, through one-on-one consultations, and by other methods. Librarians with backgrounds from art history to doctoral degrees in genetics have worked to establish these programs.
Conclusion: Successful bioinformatics support programs can be established in libraries in a variety of different settings and by staff with a variety of different backgrounds and approaches.
Data management and integration are complicated and ongoing problems that will require commitment of resources and expertise from the various biological science communities. Primary components of successful cross-scale integration are smooth information management and migration from one context to another. We call for a broadening of the definition of bioinformatics and bioinformatics training to span biological disciplines and biological scales. Training programs are needed that educate a new kind of informatics professional, Biological Information Specialists, to work in collaboration with various discipline-specific research personnel. Biological Information Specialists are an extension of the informationist movement that began within library and information science (LIS) over 30 years ago as a professional position to fill a gap in clinical medicine. These professionals will help advance science by improving access to scientific information and by freeing scientists who are not interested in data management to concentrate on their science.
The mission of the European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL) in Heidelberg, is to ensure that the growing body of information from molecular biology and genome research is placed in the public domain and is accessible freely to all parts of the scientific community in ways that promote scientific progress. To fulfil this mission, the EBI provides a wide variety of free, publicly available bioinformatics services. These can be divided into data submissions processing; access to query, analysis and retrieval systems and tools; ftp downloads of software and databases; training and education and user support. All of these services are available at the EBI website: http://www.ebi.ac.uk/services. This paper provides a detailed introduction to the interactive analysis systems that are available from the EBI and a brief introduction to other, related services.
Health care leaders emphasize the need to include information technology and informatics concepts in formal education programs, yet integration of informatics into health educational programs has progressed slowly. The AMIA 1999 Spring Congress was held to address informatics educational issues across health professions, including the educational needs in the various health professions, goals for health informatics education, and implementation strategies to achieve these goals. This paper presents the results from AMIA work groups focused on informatics education for non-informatics health professionals. In the categories of informatics needs, goals, and strategies, conference attendees suggested elements in these areas: educational responsibilities for faculty and students, organizational responsibilities, core computer skills and informatics knowledge, how to learn informatics skills, and resources required to implement educational strategies.
The development of high throughput experimental technologies have given rise to the "-omics" era where terabyte-scale datasets for systems-level measurements of various cellular and molecular phenomena pose considerable challenges in data processing and extraction of biological meaning. Moreover, it has created an unmet need for the effective integration of these datasets to achieve insights into biological systems. While it has increased the demand for bioinformatics experts who can interface with biologists, it has also raised the requirement for biologists to possess a basic capability in bioinformatics and to communicate seamlessly with these experts. This may be achieved by embedding in their undergraduate and graduate life science education, basic training in bioinformatics geared towards acquiring a minimum skill set in computation and informatics.
Based on previous attempts to define curricula suitable for addressing the bioinformatics capability gap, an initiative was taken during the Workshops on Education in Bioinformatics and Computational Biology (WEBCB) in 2008 and 2009 to identify a minimum skill set for the training of future bioinformaticians and molecular biologists with informatics capabilities. The minimum skill set proposed is cross-disciplinary in nature, involving a combination of knowledge and proficiency from the fields of biology, computer science, mathematics and statistics, and can be tailored to the needs of the "-omics".
The proposed bioinformatics minimum skill set serves as a guideline for biology curriculum design and development in universities at both the undergraduate and graduate levels.
User-centred design (UCD) is a type of user interface design in which the needs and desires of users are taken into account at each stage of the design process for a service or product; often for software applications and websites. Its goal is to facilitate the design of software that is both useful and easy to use. To achieve this, you must characterise users’ requirements, design suitable interactions to meet their needs, and test your designs using prototypes and real life scenarios.
For bioinformatics, there is little practical information available regarding how to carry out UCD in practice. To address this we describe a complete, multi-stage UCD process used for creating a new bioinformatics resource for integrating enzyme information, called the Enzyme Portal (http://www.ebi.ac.uk/enzymeportal). This freely-available service mines and displays data about proteins with enzymatic activity from public repositories via a single search, and includes biochemical reactions, biological pathways, small molecule chemistry, disease information, 3D protein structures and relevant scientific literature.
We employed several UCD techniques, including: persona development, interviews, ‘canvas sort’ card sorting, user workflows, usability testing and others. Our hope is that this case study will motivate the reader to apply similar UCD approaches to their own software design for bioinformatics. Indeed, we found the benefits included more effective decision-making for design ideas and technologies; enhanced team-working and communication; cost effectiveness; and ultimately a service that more closely meets the needs of our target audience.
3D protein structure; Biological pathways; Card sorting; Design; Enzyme; Enzyme portal; Implementation; Personae; Prototyping; User-centered design (USA spelling); User-centred design; User experience; User profiles; User requirements; Usability testing
The mainstream application of massively parallel, high-throughput assays in
biomedical research has created a demand for scientists educated in
Computational Biology and Bioinformatics (CBB). In response, formalized graduate
programs have rapidly evolved over the past decade. Concurrently, there is
increasing need for clinicians trained to oversee the responsible translation of
CBB research into clinical tools. Physician-scientists with dedicated CBB
training can facilitate such translation, positioning themselves at the
intersection between computational biomedical research and medicine. This
perspective explores key elements of the educational path to such a position,
specifically addressing: 1) evolving perceptions of the role of the
computational biologist and the impact on training and career opportunities; 2)
challenges in and strategies for obtaining the core skill set required of a
biomedical researcher in a computational world; and 3) how the combination of
CBB with medical training provides a logical foundation for a career in academic
medicine and/or biomedical research.
computational biology; bioinformatics; graduate education; MD/PhD
Background: The information landscape in biological and medical research has grown far beyond literature to include a wide variety of databases generated by research fields such as molecular biology and genomics. The traditional role of libraries to collect, organize, and provide access to information can expand naturally to encompass these new data domains.
Methods: This paper discusses the current and potential role of libraries in bioinformatics using empirical evidence and experience from eleven years of work in user services at the National Center for Biotechnology Information.
Findings: Medical and science libraries over the last decade have begun to establish educational and support programs to address the challenges users face in the effective and efficient use of a plethora of molecular biology databases and retrieval and analysis tools. As more libraries begin to establish a role in this area, the issues they face include assessment of user needs and skills, identification of existing services, development of plans for new services, recruitment and training of specialized staff, and establishment of collaborations with bioinformatics centers at their institutions.
Conclusions: Increasing library involvement in bioinformatics can help address information needs of a broad range of students, researchers, and clinicians and ultimately help realize the power of bioinformatics resources in making new biological discoveries.
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) serves a community of users with diverse backgrounds and interests. In addition to processing, archiving and distributing structural data, it also develops educational resources and materials to enable people to utilize PDB data and to further a structural view of biology.
The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB) supports scientific research and education worldwide by providing an essential resource of information on biomolecular structures. In addition to serving as a deposition, data-processing and distribution center for PDB data, the RCSB PDB offers resources and online materials that different audiences can use to customize their structural biology instruction. These include resources for general audiences that present macromolecular structure in the context of a biological theme, method-based materials for researchers who take a more traditional approach to the presentation of structural science, and materials that mix theme-based and method-based approaches for educators and students. Through these efforts the RCSB PDB aims to enable optimal use of structural data by researchers, educators and students designing and understanding experiments in biology, chemistry and medicine, and by general users making informed decisions about their life and health.
Protein Data Bank; crystallographic education; macromolecular structures; biological crystallography
Support for molecular biology researchers has been limited to traditional library resources and services in most academic health sciences libraries. The University of Washington Health Sciences Libraries have been providing specialized services to this user community since 1995. The library recruited a Ph.D. biologist to assess the molecular biological information needs of researchers and design strategies to enhance library resources and services. A survey of laboratory research groups identified areas of greatest need and led to the development of a three-pronged program: consultation, education, and resource development. Outcomes of this program include bioinformatics consultation services, library-based and graduate level courses, networking of sequence analysis tools, and a biological research Web site. Bioinformatics clients are drawn from diverse departments and include clinical researchers in need of tools that are not readily available outside of basic sciences laboratories. Evaluation and usage statistics indicate that researchers, regardless of departmental affiliation or position, require support to access molecular biology and genetics resources. Centralizing such services in the library is a natural synergy of interests and enhances the provision of traditional library resources. Successful implementation of a library-based bioinformatics program requires both subject-specific and library and information technology expertise.
There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences.
Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant.
Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence annotations relating to a gene, its transcripts and translations. The mechanism of transcript definition and creation, and subsequent navigation and exploration of features, are very intuitive and demand only a short learning curve. Ultimately, Djinn Lite can form the basis for providing valuable clues to plan new experiments, providing storage of sequences and annotations for dedication to customised projects. The application is appropriate for Windows 98-ME-2000-XP-2003 operating systems.
The arrival of a computerized medical information system on the health care scene has created new performance demands on nurses. Not only must nurses be able to use the computer to document medical and nursing care, but they must be able to contribute to the overall design of the nursing data base. This paper describes how nurses must be educated to perform these new job responsibilities. Discussion will center on the educational process developed by the Clinical Center at the National Institutes of Health to meet the needs of its nurses to design a nursing data base and learn the technical skill required to utilize a computerized medical information system. Recommendations are offered to the academic community charged with the formal education of nursing professionals and the staff development and continuing educational planners who share the accountability for educating the already licensed nurses.
Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or sequence properties compared to another group, and whether this enrichment is statistically significant. In order to conduct such comparisons it is often required to integrate molecular sequence data and experimental information from disparate incompatible sources. While many specialized programs exist for comparisons of this kind in individual problem domains, such as expression data analysis, no generic software solution capable of addressing a wide spectrum of routine tasks in comparative proteomics is currently available.
PROMPT is a comprehensive bioinformatics software environment which enables the user to compare arbitrary protein sequence sets, revealing statistically significant differences in their annotation features. It allows automatic retrieval and integration of data from a multitude of molecular biological databases as well as from a custom XML format. Similarity-based mapping of sequence IDs makes it possible to link experimental information obtained from different sources despite discrepancies in gene identifiers and minor sequence variation. PROMPT provides a full set of statistical procedures to address the following four use cases: i) comparison of the frequencies of categorical annotations between two sets, ii) enrichment of nominal features in one set with respect to another one, iii) comparison of numeric distributions, and iv) correlation of numeric variables. Analysis results can be visualized in the form of plots and spreadsheets and exported in various formats, including Microsoft Excel.
PROMPT is a versatile, platform-independent, easily expandable, stand-alone application designed to be a practical workhorse in analysing and mining protein sequences and associated annotation. The availability of the Java Application Programming Interface and scripting capabilities on one hand, and the intuitive Graphical User Interface with context-sensitive help system on the other, make it equally accessible to professional bioinformaticians and biologically-oriented users. PROMPT is freely available for academic users from .
Microbial metagenomic analyses rely on an increasing number of publicly available tools. Installation, integration, and maintenance of the tools poses significant burden on many researchers and creates a barrier to adoption of microbiome analysis, particularly in translational settings.
To address this need we have integrated a rich collection of microbiome analysis tools into the Genboree Microbiome Toolset and exposed them to the scientific community using the Software-as-a-Service model via the Genboree Workbench. The Genboree Microbiome Toolset provides an interactive environment for users at all bioinformatic experience levels in which to conduct microbiome analysis. The Toolset drives hypothesis generation by providing a wide range of analyses including alpha diversity and beta diversity, phylogenetic profiling, supervised machine learning, and feature selection.
We validate the Toolset in two studies of the gut microbiota, one involving obese and lean twins, and the other involving children suffering from the irritable bowel syndrome.
By lowering the barrier to performing a comprehensive set of microbiome analyses, the Toolset empowers investigators to translate high-volume sequencing data into valuable biomedical discoveries.
The Second Symposium on Computations in Bioinformatics and Bioscience (SCBB07) was held in Iowa City, Iowa, USA, on August 13–15, 2007. This annual event attracted dozens of bioinformatics professionals and students, who are interested in solving emerging computational problems in bioscience, from China, Japan, Taiwan and the United States. The Scientific Committee of the symposium selected 18 peer-reviewed papers for publication in this supplemental issue of BMC Bioinformatics. These papers cover a broad spectrum of topics in computational biology and bioinformatics, including DNA, protein and genome sequence analysis, gene expression and microarray analysis, computational proteomics and protein structure classification, systems biology and machine learning.
Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involved have to be able to work with each other's data – therefore, a common set of well-defined data formats is needed. Unfortunately, current bioinformatic tools use a great variety of heterogeneous formats.
Acknowledging the need for common formats, the Helmholtz Open BioInformatics Technology network (HOBIT) identified several basic data types used in bioinformatics and developed appropriate format descriptions, formally defined by XML schemas, and incorporated them in a Java library (BioDOM). These schemas currently cover sequence, sequence alignment, RNA secondary structure and RNA secondary structure alignment formats in a form that is independent of any specific program, thus enabling seamless interoperation of different tools. All XML formats are available at , the BioDOM library can be obtained at .
The HOBIT XML schemas and the BioDOM library simplify adding XML support to newly created and existing bioinformatic tools, enabling these tools to interoperate seamlessly in workflow scenarios.
Setting: Purdue University is a major agricultural, engineering, biomedical, and applied life science research institution with an increasing focus on bioinformatics research that spans multiple disciplines and campus academic units. The Purdue University Libraries (PUL) hired a molecular biosciences specialist to discover, engage, and support bioinformatics needs across the campus.
Program Components: After an extended period of information needs assessment and environmental scanning, the specialist developed a week of focused bioinformatics instruction (Bioinformatics Week) to launch system-wide, library-based bioinformatics services.
Evaluation Mechanisms: The specialist employed a two-tiered approach to assess user information requirements and expectations. The first phase involved careful observation and collection of information needs in-context throughout the campus, attending laboratory meetings, interviewing department chairs and individual researchers, and engaging in strategic planning efforts. Based on the information gathered during the integration phase, several survey instruments were developed to facilitate more critical user assessment and the recovery of quantifiable data prior to planning.
Next Steps/Future Directions: Given information gathered while working with clients and through formal needs assessments, as well as the success of instructional approaches used in Bioinformatics Week, the specialist is developing bioinformatics support services for the Purdue community. The specialist is also engaged in training PUL faculty librarians in bioinformatics to provide a sustaining culture of library-based bioinformatics support and understanding of Purdue's bioinformatics-related decision and policy making.
With the advent of YouTube channels in bioinformatics, open platforms for problem solving in bioinformatics, active web forums in computing analyses and online resources for learning to code or use a bioinformatics tool, the more traditional continuing education bioinformatics training programs have had to adapt. Bioinformatics training programs that solely rely on traditional didactic methods are being superseded by these newer resources. Yet such face-to-face instruction is still invaluable in the learning continuum. Bioinformatics.ca, which hosts the Canadian Bioinformatics Workshops, has blended more traditional learning styles with current online and social learning styles. Here we share our growing experiences over the past 12 years and look toward what the future holds for bioinformatics training programs.
continuing education; bioinformatics; online learning; massive open online courses (MOOCs)
As the volume, complexity and diversity of the information that scientists work with on a daily basis continues to rise, so too does the requirement for new analytic software. The analytic software must solve the dichotomy that exists between the need to allow for a high level of scientific reasoning, and the requirement to have an intuitive and easy to use tool which does not require specialist, and often arduous, training to use. Information visualization provides a solution to this problem, as it allows for direct manipulation and interaction with diverse and complex data. The challenge addressing bioinformatics researches is how to apply this knowledge to data sets that are continually growing in a field that is rapidly changing.
This paper discusses an approach to the development of visual mining tools capable of supporting the mining of massive data collections used in systems biology research, and also discusses lessons that have been learned providing tools for both local researchers and the wider community. Example tools were developed which are designed to enable the exploration and analyses of both proteomics and genomics based atlases. These atlases represent large repositories of raw and processed experiment data generated to support the identification of biomarkers through mass spectrometry (the PeptideAtlas) and the genomic characterization of cancer (The Cancer Genome Atlas). Specifically the tools are designed to allow for: the visual mining of thousands of mass spectrometry experiments, to assist in designing informed targeted protein assays; and the interactive analysis of hundreds of genomes, to explore the variations across different cancer genomes and cancer types.
The mining of massive repositories of biological data requires the development of new tools and techniques. Visual exploration of the large-scale atlas data sets allows researchers to mine data to find new meaning and make sense at scales from single samples to entire populations. Providing linked task specific views that allow a user to start from points of interest (from diseases to single genes) enables targeted exploration of thousands of spectra and genomes. As the composition of the atlases changes, and our understanding of the biology increase, new tasks will continually arise. It is therefore important to provide the means to make the data available in a suitable manner in as short a time as possible. We have done this through the use of common visualization workflows, into which we rapidly deploy visual tools. These visualizations follow common metaphors where possible to assist users in understanding the displayed data. Rapid development of tools and task specific views allows researchers to mine large-scale data almost as quickly as it is produced. Ultimately these visual tools enable new inferences, new analyses and further refinement of the large scale data being provided in atlases such as PeptideAtlas and The Cancer Genome Atlas.
Objective: User data and information about anatomy education were used to guide development of a learning environment that is efficient and effective. The research question focused on how to design instructional software suitable for the educational goals of different groups of users of the Visible Human data set. The ultimate goal of the study was to provide options for students and teachers to use different anatomy learning modules corresponding to key topics, for course work and professional training.
Design: The research used both qualitative and quantitative methods. It was driven by the belief that good instructional design must address learning context information and pedagogic content information. The data collection emphasized measurement of users' perspectives, experience, and demands in anatomy learning.
Measurement: Users' requirements elicited from 12 focus groups were combined and rated by 11 researchers. Collective data were sorted and analyzed by use of multidimensional scaling and cluster analysis.
Results: A set of functions and features in high demand across all groups of users was suggested by the results. However, several subgroups of users shared distinct demands. The design of the learning modules will encompass both unified core components and user-specific applications. The design templates will allow sufficient flexibility for dynamic insertion of different learning applications for different users.
Conclusion: This study describes how users' requirements, associated with users' learning experiences, were systematically collected and analyzed and then transformed into guidelines informing the iterative design of multiple learning modules. Information about learning challenges and processes was gathered to define essential anatomy teaching strategies. A prototype instrument to design and polish the Visible Human user interface system is currently being developed using ideas and feedback from users.
Rapid increase in protein sequence information from genome sequencing projects demand the intervention of bioinformatics tools to recognize interesting gene-products and associated
function. Often, multiple algorithms need to be employed to improve accuracy in predictions and several structure prediction algorithms are on the public domain. Here, we report the
availability of an Integrated Web-server as a bioinformatics online package dedicated for in-silico analysis of protein sequence and structure data (IWS). IWS provides web interface
to both in-house and widely accepted programs from major bioinformatics groups, organized as 10 different modules. IWS also provides interactive images for Analysis Work Flow, which
will provide transparency to the user to carry out analysis by moving across modules seamlessly and to perform their predictions in a rapid manner.
IWS is available from the URL: http://caps.ncbs.res.in/iws.
protein sequence; structure analysis
MCBIOS is a regional bioinformatics society founded in 2002. Its mission is to foster networking and collaboration, and promote the professional development of its members with a strong orientation toward supporting our students. We seek to: 1) Advance the understanding of bioinformatics and computational biology; 2) Bring together scientists of various backgrounds and disciplines; 3) Facilitate the collaboration of researchers with similar or complementary backgrounds to solve biological, health, and/or medical problems; 4) Promote education in bioinformatics and computational biology; 5) Inform the general public on the results and implications of current research in bioinformatics and computational biology; and 6) Promote other activities that will contribute to the development of bioinformatics and computational biology. While centered in a region encompassing Arkansas, Louisiana, Mississippi, Missouri, Oklahoma, western Tennessee, and eastern Texas, attendees at our annual conferences come from close to half the states in the US. These conferences are held early in the Spring semester and feature well-known keynote speakers. For more information, please visit www.MCBIOS.org and a related article on “Regional Societies: Fostering Competitive Research Through Virtual Infrastructures” at http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.0020372.
Objective: To provide an overview of current issue and research literature that discusses the use of eLearning in an academic curriculum. We address several components to be examined before eLearning is incorporated into athletic training education.
Data Sources: We searched MEDLINE and Educational Resources Information Center (ERIC) from 2000 through 2002 using the key words distance education, online learning, and the individual research studies referenced in this article.
Data Synthesis: Educational research studies have confirmed that multiple methods in instruction delivery exist. Within the changing culture of higher education, the use of effective communication tools has been shown to increase student knowledge and skills. Through eLearning, methods of instruction design are designed to be student centered and allow the educator to become a facilitator.
Conclusions/Recommendations: Even though the use of eLearning faces many challenges in athletic training education, the research literature does support this method of instructional delivery in selected courses in athletic training education.
cybergogy; distance education; student centered
Many bioinformatics algorithms and data sets are deployed using web services so that the results can be explored via the Internet and easily integrated into other tools and services. These services often include data from other sites that is accessed either dynamically or through file downloads. Developers of these services face several problems because of the dynamic nature of the information from the upstream services. Many publicly available repositories of bioinformatics data frequently update their information. When such an update occurs, the developers of the downstream service may also need to update. For file downloads, this process is typically performed manually followed by web service restart. Requests for information obtained by dynamic access of upstream sources is sometimes subject to rate restrictions.
SideCache provides a framework for deploying web services that integrate information extracted from other databases and from web sources that are periodically updated. This situation occurs frequently in biotechnology where new information is being continuously generated and the latest information is important. SideCache provides several types of services including proxy access and rate control, local caching, and automatic web service updating.
We have used the SideCache framework to automate the deployment and updating of a number of bioinformatics web services and tools that extract information from remote primary sources such as NCBI, NCIBI, and Ensembl. The SideCache framework also has been used to share research results through the use of a SideCache derived web service.