We hereby would like to share our testplan for testing most of the functionalities of Phenotype database version 2.
Phenotype db V2 Generic testplan
On the tab “General” the setup and way to use this testplan is explained. Please feel free to add corrections or remarks in this file.
The files mentioned in the testplan can be found here:
Testplan files for import
Software support and tester at The Hyve
Jolanda has a Master degree in Chemistry from the University of Utrecht in the field of Biochemistry. She has extensive experience as a data manager in Clinical Trials and Investigator Initiated medical studies, both in a commercial and an academic setting.
At the Hyve she provides functional support to users of applications developed and/or supported by The Hyve. She is also involved testing (newly developed) software and creating user documentation on this software.
Project manager at the Hyve
Jochem studied Biomedical Sciences and Bioinformatics. He has done research projects in the field of computational systems biology and molecular dynamics computer simulations.
As an intern at The Hyve he finished his master’s degree with a focus on technical requirements for the integration of different molecular data types (e.g. from genomics, transcriptomics, proteomics). He then joined The Hyve as a data scientist and is currently working as a Project manager.
Developer at The Hyve
Peter studied Computer Science at the TU Delft and obtained a PhD degree from the same university in 2014. For his PhD he investigated methods for integrative visualization for whole body molecular imaging data. This work focused on multi-modality registration, fusion and visualization of bioluminescence imaging data, which is applied in cancer research to monitor tumor growth. This was a collaboration with the image processing department (LKEB) at the Leiden University Medical Center.
His interests are in the fields of computer graphics, scientific and information visualization, machine learning and the application of these in life sciences and other scientific fields. He also has experience as a freelance software developer, doing various types of projects ranging from mobile app development to projects in medical visualization.
This is a short presentation on what Phenotype database is, who it is for and how it works.
Phenotype database presentation- what is it
A new and improved version of the Phenotype database is available. The main changes compared to V1 are:
- New User Interface
- Introduced a timeline to the “Design” part, to simplify study design
- New importer with many performance improvements
- Many fixes to the analyses/visualization functionality
- Improvement of displaying large amounts of data
- Updated short and extended manual
Click here for the source code
Click here for the short manual
Click here for the extended manual
The exact organisation and legal structure of the Phenotype Foundation is still being discussed. Anything on this website is subject to change.
The scientists and analysts who use the Phenotype Foudation software and set out its future course.
The programmers and bioinformaticians who contribute to the various projects that are hosted at the Foundation
The Phenotype Foundation mission is to empower scientists, within various communities of practice, with standardized software and knowledge stores to store, manage, and retrieve information and data on genotypes and phenotypes.
Achieving this mission requires the completion of four complimentary aims:
- Include the existing study database initiatives.
- Identify, recruit, and organize appropriate scientists into communities of practice who will benefit from the development and use of standardized knowledge stores and software for the purposes of characterizing phenotypes from studies.
- Utilize the knowledge and expertise of these identified scientists to guide the design and development of the software and knowledge repositories capable of assisting in the characterization of phenotypes.
- Structure and create the necessary databases and software the programming.
We have identified critical initial and continuing requirements that will be addressed by the Phenotype Foundation:
- A governance and decision-making structure for community commodities (i.e. the data and databases);
- A Scientific Advisory Board to enumerate and characterize the scientific priorities and needs of the Phenotype Foundation;
- A Technical Advisory Board, to guide the dbXP platform hosting decisions, as well as design and development trajectories;
- Neutral and sustainable ownership of code, trademarks and domains for all dbXP software and databases;
- Be a representative entity for the promotion and use of dbXP software and database structure;
- Initiate, guide, and interact with relevant bioinformatics and database owning organisations;
- Ensure continuous hosting and maintenance of all public dbXP databases;
- Raise funds to support the above activities.
- The Phenotype Foundation is governed by a Board of Directors (BOD) to be elected every two years with two being elected in any given year.
- The BOD shall be comprised of seven Foundation members with at least one member representing the Technical Advisory Board, and at least one member representing the Scientific Advisory Board.
- The Board of Directors will meet at least twice per year.
- Scientific and Technical Advisory Boards will each meet at least every month
- The main tasks of the Board of Directors are to define, refine and implement the strategy of the Foundation as mentioned above, and specifically to set and update the roadmap for dbXP software development that is carried out by the Programmers Community.
- Membership of the Foundation is open to everyone who shows active participation in dbXP (e.g. uploading of data, programming of modules, acquirement of funding).
- Membership applications are decided upon by current Foundation members
- The Members of the Foundation elect their Board every two years.
Dr. Chris Evelo is the head of the Department of Bioinformatics – BiGCaT at Maastricht University. He is author and co-author of more than 70 publications in the field of bioinformatics, systems biology and toxicology. His main research focus is on integrative systems biology where he uses modern bioinformatics approaches to understand different types of genomics, metabolomics and large scale genetics data by combining it with what we already know.
He is a council member of the Research School for Nutrition and Toxicology in Maastricht and the European Network of Excellence for Nutrigenomics and leading the bioinformatics in that program and a a member of the steering committee of the IMI program Open Phacts, he is also in the coordinating teams for the micronutrient genomics program and for the development of the nutritional phenotype database. Dr. Evelo is also involved in co-ordinating teaching programs related to bioinformatics such as the EU funded Biohealth Computing initiative.
GSCF is the main module of dbNP, the Nutritional Phenotype Database software project that was initiatied by NuGO, and further carried on within Netherlands Metabolomics Centre and Netherlands Bioinformatics Centre.
Click here for source code
Click here for the GSCF User Guide (PDF)
The Clean Transcriptomics Database is a module of the Nutritional Phenotype Database (dbNP). The development of this module is funded by NuGO and built by Wageningen University & Research Centre. It aims at a centralized storage of transcriptomics data, that is queryable via the dbNP query module, and has its accompanying study metadata stored in the dbNP study capture module (GSCF, see under).
It complies with the ‘dbNP omics submodule’ standard by serving clean data via the dbNP clean data layer.
Click here for source code
The metagenomics module, attached to GSCF, stores genetic sequencing data derived from environmental samples, such as bacteria.
The metagenomics module is developed in the ANTIRESDEV project, which receives funding from EU FP7. Among others, its aim is to gain knowledge of the dynamics of resistance emergence at a variety of body sites during the administration of a range of antibiotics frequently used in Europe.
Click here for source code
Click here for poster
The metabolomics module functions as a repository of metabolomics data, facilitating storage of raw and processed metabolomics data and study information, which can be searched and queried.
This module is part of the NMC DSP, a data support platform for metabolomics studies built by Netherlands Metabolomics Centre (NMC), to support storage of experimental metabolomics data, and their processing. This bioinformatics support platform will provide a means for communication between the partners of the NMC for the exchange of data, software, and tools. (See also our portfolio.)
Click here for source code
Click here for the Metabolomics User Guide (PDF)
The Nutritional Phenotype project (dbNP) is an open source ecosystem for multi-omics databases. One of the modules of dbNP is the Simple assay module (SAM), in which it is easy to import bulk numerical data from e.g. Excel files. It is used to store clinical data, such as Rules Based Medicine assays, but also physical measurements such as body weight of mice. Continue reading
Kees van Bochove owns a company dedicated to the support and facilitation of sustainable open source bioinformatics software development (The Hyve). As technical project manager of the global dbNP open source initiative, he leads the development of several Phenotype Foundation software projects. Also, Kees is metabolomics taskforce leader in the NBIC Central Engineering Team and technical project manager of the Data Support Platform project of the NMC. Kees holds bachelor’s degrees in computer science and in primary education, and a master’s degree in bioinformatics, for which he did his research project on lipoprotein metabolism at the Jean Mayer USDA Human Nutrition Research Center on Aging at Tufts University, Boston.
Scientist at TNO
Jildau Bouwman (born in Heemskerk, The Netherlands in 1976, PhD in 2006 at VU University, in The Netherlands) is a molecular biologist who has used informatics in biological research were needed. She has done research in several organisms (mouse, yeast and human), with a focus on omics technologies (transcriptomics and metabolomics). Working on the IOP project ‘Vertical genomics’ at the VU University made her aware that linking different information sources is essential to be able to perform systems biology. She is one of the driving forces behind the phenotype application and principle investigator in the Netherlands Metabolomics Centre Data support platform.
Since 2008 she is working at TNO in the group of Microbiology and Systems Biology and is theme leader knowledge basing. She is involved in several European projects that are performing systems biology studies (Food4me, Eurreca, NuAge).