IBM makes a rich set of sample applications available. We recommend adding them during the WAS installation. One such application is Plants by IBM WebSphere storefront. Its customers can open accounts, browse for items to purchase, view product details, and place orders. Plants by IBM WebSphere uses container-managed persistence (CMP), container-managed relationships (CMR), stateless session beans, a stateful session bean, JSP pages, and servlets.

It aims to be production ready, out of the box. As part of this, Spring Boot does a few things differently, by default, that may be at first alien to some. In this post, I hope to briefly cover some of the common strategies for deploying a Spring Boot applications. I'll ever so briefly introduce it, and some sample code, before we dive deeper. Feel free to skip this section and start at the Embedded Web Server Deployment section.


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In PiiMS, we have developed workflow controls and data storage systems to facilitate the high-throughput data acquisition required by our ionomics projects. PiiMS models the physical workflow in the laboratory and divides it into stages based on the physical activities and the information and data generated throughout the experiment life cycle. In this way, it can provide workflow management support as well as the capability to capture contextual information (metadata) necessary to fully describe the experiment. This system allows us to control and capture, through a series of input portals, the flow of information in our high-throughput ionomics system. Information mapping the position of the plants in the experimental unit to the sample analysis vial is captured, helping to reduce errors in sample identification after analysis. Information relating to the plant's genotype and genealogy, date planted and harvested, environmental, and ICP-MS analytical conditions are also captured. After ICP-MS analysis is completed, all analytical data are uploaded into PiiMS via a Web-based upload portal. All experimental metadata and ICP-MS analytical data are associated in the database. Tools are also implemented in the system to manage various aspects of the PiiMS environment, including creation of new sample maps, addition of new genetic and genealogy information, and management of users and instruments. Within our Ionomics project, PiiMS is used daily to manage a continuous functional genomics pipeline containing over 3,000 active samples. PiiMS manages plant growth, harvest, sample preparation, and ICP-MS analysis and is used daily to analyze and store over 2,000 fully quantified elemental concentrations. PiiMS also provides on demand data reanalysis and open access search and retrieval capability across the complete ionomics dataset. Similar ideas for the development of supportive data collection tools for plant metabolomics have recently been proposed (Jenkins et al., 2005), but to our knowledge PiiMS is the first true implementation of these ideas integrated into an existing high-throughput analytical phenotyping platform.

The concept of open access has long been a part of science because scientists share their reagents, mutants, and protocols. However, usually researchers only share the final products of their research. For example, researchers who conduct genetic screens generally only share the lines that they identified as mutants. The complete dataset from the screens is usually not shared. Taking advantage of the ability of PiiMS to display data for every sample that we have run, we have designed a screening protocol that enables anyone to view the primary data from our screens and rerun lines that were not initially selected. This enables open access to the process, which we hope will result in better mutant identification. The two EMS screens were conducted using the open access mutant identification protocol. Of the approximately 1,600 M2 plants screened under each condition, we identified putative mutants by visual inspection of z-score plots (see section on data visualization) and collected seed from selected individual plants (178 plants in the Fe screen and 233 in the P screen). All other M2 plants were grown and harvested in rows so the seed from six to 12 plants is bulked into a single tube. If users identify additional putative mutants using data in PiiMS, either by visual inspection of an ionomic phenotype of interest or through new bioinformatics algorithms, these pools can be easily screened to reidentify the putative mutant. Of the 178 EMS Fe putative mutants, 137 produced seed and were reanalyzed. From visual inspection of z-score plots, we identified 56 lines as confirmed mutants that will be deposited in the ABRC. Several confirmed mutants have also been backcrossed to Col-0 and outcrossed to Landsberg erecta (Ler-0) for mapping and the data from F1 and F2 populations are also contained in the database.

In order to illustrate the WebSphere Liberty application server integration, the following sections will highlight the required Liberty configuration changes, and provide sample code for sending and receiving messages using Enterprise Java Beans. e24fc04721

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