Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2011 Oct 31:12:425.
doi: 10.1186/1471-2105-12-425.

MolabIS--an integrated information system for storing and managing molecular genetics data

Cong V C Truong  1 , Linn F Groeneveld, Burkhard Morgenstern, Eildert Groeneveld
Affiliations

MolabIS--an integrated information system for storing and managing molecular genetics data

Cong V C Truong et al. BMC Bioinformatics. .

Abstract

Background: Long-term sample storage, tracing of data flow and data export for subsequent analyses are of great importance in genetics studies. Therefore, molecular labs do need a proper information system to handle an increasing amount of data from different projects.

Results: We have developed a molecular labs information management system (MolabIS). It was implemented as a web-based system allowing the users to capture original data at each step of their workflow. MolabIS provides essential functionality for managing information on individuals, tracking samples and storage locations, capturing raw files, importing final data from external files, searching results, accessing and modifying data. Further important features are options to generate ready-to-print reports and convert sequence and microsatellite data into various data formats, which can be used as input files in subsequent analyses. Moreover, MolabIS also provides a tool for data migration.

Conclusions: MolabIS is designed for small-to-medium sized labs conducting Sanger sequencing and microsatellite genotyping to store and efficiently handle a relative large amount of data. MolabIS not only helps to avoid time consuming tasks but also ensures the availability of data for further analyses. The software is packaged as a virtual appliance which can run on different platforms (e.g. Linux, Windows). MolabIS can be distributed to a wide range of molecular genetics labs since it was developed according to a general data model. Released under GPL, MolabIS is freely available at http://www.molabis.org.

PubMed Disclaimer

Figures

Figure 1
Figure 1
Entity-Relationship diagram of MolabIS. Entity-Relationship diagram using Crow's Foot notation presents the conceptual data structure used in MolabIS. Entities and relationships are represented as boxes and lines between the boxes, respectively. The database structure consists of 23 tables presented in three groups (three different colors). To simplify the complexity of the data model, foreign keys which are linked to Codes and Protocols are not shown.
Figure 2
Figure 2
Management of sample storage. A five level storage schema is used to manage the location of samples. It is constructed as a tree model. The highest level (level 1) is the storage location. The lowest level (level 5) is the sample storage. The middle levels (level 2, level 3 and level 4) may be different among labs. The labels in all levels are defined by users.
Figure 3
Figure 3
Application architecture. MolabIS is based on a three-tier client/server architechture including presentation tier, application tier and data tier.
Figure 4
Figure 4
Main user interface. MolabIS provides five different modules which can be accessed from the menu bar in the main interface. From left to right, these modules are Workflow, Manage Data, Reports, Export Data and Administration. Each module consists of many sub-modules which allow users to communicate with the system via web forms.
Figure 5
Figure 5
Data flows for capturing data in MolabIS. Data can be entered into the database through either a series of web forms under the workflow or a batch loading mode. The former is suited for inserting data of new projects while the latter is often used for data migration. The workflow feature of MolabIS enables users to insert or import a large number of data records via dynamic web forms. A form can consist of a sequence of sub-forms.
Figure 6
Figure 6
GUI for uploading DNA samples. The screenshot presents a sequence of web forms for inserting DNA samples into the database. Step 1: identify the number of samples which will be uploaded (e.g. 5); Step 2: enter data manually for all samples or upload data from the spreadsheet; Step 3: provide information on DNA validation and upload gel images (this step can be skipped if DNA samples are not checked); Step 4: select the storage locations of DNA samples.
Figure 7
Figure 7
GUI for importing microsatellite data. The screenshot shows an example of improrting microsatellite data for 134 samples of a project. Step 1: identify samples of a project and select markers; Step 2: import microsatellite data from a spreadsheet and upload to the server.
Figure 8
Figure 8
Data association. Relationship between associated data objects for keeping track of samples, and results.
Figure 9
Figure 9
GUI for extracting sequence data to various formats. Sequences can be extracted and converted to different data formats. The GUI shows that users can select sequences from different projects for a specific marker to be merged into a multiple sequence file by clicking on a respective button at the bottom of the form. After pressing the button, the system will generate a file in a desired format which is available for download.
Figure 10
Figure 10
GUI for extracting microsatellite data to various formats. MolabIS can convert microsatellite data of a given project to various formats. The GUI shows that users can select a data format and a file format from drop-down lists for the output, identify markers and samples and click on the "Export" button to download the file.
See this image and copyright information in PMC

Similar articles

See all similar articles

Cited by

References

    1. Vignala A, Milana D, SanCristobal M, Eggen A. A review on SNP and other types of molecular markers and their use in animal genetics. Genet Sel Evol. 2002;34(3):275–305. doi: 10.1186/1297-9686-34-3-275. - DOI - PMC - PubMed
    1. Baumung R, Simianer H, Hoffmann I. Genetic diversity studies in farm animals - a survey. J of Anim Breed and Genet. 2004;121(6):361–373. doi: 10.1111/j.1439-0388.2004.00479.x. - DOI
    1. Rudd S, Schoof H, Mayer K. PlantMarkers: a database of predicted molecular markers from plants. Nucleic Acids Res. 2005;33:628–632. - PMC - PubMed
    1. Rosenberg NA, Burke T, Elo K, Feldman MW, Freidlin PJ, Groenen MA, Hillel J, Maki-Tanila A, Tixier-Boichard M, Vignal A, Wimmers K, Weigend S. Empirical Evaluation of Genetic Clustering Methods Using Multilocus Genotypes From 20 Chicken Breeds. Genetics. 2001;159(2):699–713. - PMC - PubMed
    1. Granevitze Z, Hillel J, Chen GH, Cuc NTK, Feldman M, Eding H, Weigend S. Genetic diversity within chicken populations from different continents and management histories. Animal Genetics. 2007;36(6):576–583. - PubMed

Publication types

LinkOut - more resources