Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps

Microarrays are a very powerful tool for quantifying the amount of RNA in samples; however, their ability to query essentially every gene in a genome, which can number in the tens of thousands, presents analytical and interpretative problems. As a result, a variety of software and web-based tools have been developed to help with these issues. This article highlights and reviews some of the tools for the first steps in the analysis of a microarray study. We have tried for a balance between free and commercial systems. We have organized the tools by topics including image processing tools (Section 2), power analysis tools (Section 3), image analysis tools (Section 4), database tools (Section 5), databases of functional information (Section 6), annotation tools (Section 7), statistical and data mining tools (Section 8), and dissemination tools (Section 9).

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The PATRIC Bioinformatics Resource Center: expanding data and analysis capabilities

Nucleic Acids Research ◽

10.1093/nar/gkz943 ◽

2019 ◽

Cited By ~ 12

Author(s):

James J Davis ◽

Alice R Wattam ◽

Ramy K Aziz ◽

Thomas Brettin ◽

Ralph Butler ◽

...

Keyword(s):

Comparative Analysis ◽

Cost Effective ◽

Command Line ◽

Web Based ◽

The Public ◽

Bioinformatic Tools ◽

Resource Center ◽

Bioinformatics Resource ◽

Analysis Tools ◽

Analysis Environment

Abstract The PathoSystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center funded by the National Institute of Allergy and Infectious Diseases (https://www.patricbrc.org). PATRIC supports bioinformatic analyses of all bacteria with a special emphasis on pathogens, offering a rich comparative analysis environment that provides users with access to over 250 000 uniformly annotated and publicly available genomes with curated metadata. PATRIC offers web-based visualization and comparative analysis tools, a private workspace in which users can analyze their own data in the context of the public collections, services that streamline complex bioinformatic workflows and command-line tools for bulk data analysis. Over the past several years, as genomic and other omics-related experiments have become more cost-effective and widespread, we have observed considerable growth in the usage of and demand for easy-to-use, publicly available bioinformatic tools and services. Here we report the recent updates to the PATRIC resource, including new web-based comparative analysis tools, eight new services and the release of a command-line interface to access, query and analyze data.

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mDAG: a web-based tool for analyzing microarray data with multiple treatments

BMC Bioinformatics ◽

10.1186/1471-2105-12-s7-a7 ◽

2011 ◽

Vol 12 (S7) ◽

Author(s):

Vinhthuy T Phan ◽

Nam S Vo ◽

Thomas R Sutter

Keyword(s):

Microarray Data ◽

Web Based ◽

Multiple Treatments

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Web Based Distance Learning Environment To Teach Computer Aided Engineering Design And Analysis Tools

10.18260/1-2--10191 ◽

2020 ◽

Author(s):

Keith Adolphson ◽

Rujin Cheng ◽

Kurt Gramoll

Keyword(s):

Distance Learning ◽

Learning Environment ◽

Engineering Design ◽

Computer Aided Engineering ◽

Web Based ◽

Analysis Tools ◽

Computer Aided ◽

Distance Learning Environment

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Stanford CyberLab

Online and Distance Learning ◽

10.4018/978-1-59904-935-9.ch194 ◽

2011 ◽

pp. 2400-2415 ◽

Cited By ~ 2

Author(s):

Lambertus Hesselink ◽

Dharmarus Rizal ◽

Eric Bjornson ◽

Sandy Paik ◽

Raj Batra ◽

...

Keyword(s):

Distance Learning ◽

Data Acquisition ◽

Data Acquisition System ◽

Acquisition System ◽

Stanford University ◽

Web Based ◽

System A ◽

Research And Teaching ◽

Analysis Tools ◽

Learning Programs

Cyberlab is a fully automated, Internet accessible laboratory for use in research and teaching, developed at Stanford University since 1996. Cyberlab is a completely self-contained system including a web-based scheduler, analysis tools, a data acquisition system, a digital notebook, extensive collaboration tools including simultaneous access to the equipment by multiple students, extensive security features, including firewall compliance without the need for IT intervention. The system is easily scalable and can be integrated with other distance learning programs.

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Tools for generating and analyzing glycan microarray data

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.16.187 ◽

2020 ◽

Vol 16 ◽

pp. 2260-2271

Author(s):

Akul Y Mehta ◽

Jamie Heimburg-Molinaro ◽

Richard D Cummings

Keyword(s):

Microarray Data ◽

Automated Analysis ◽

Experimental Methods ◽

Vital Role ◽

Data Repositories ◽

Glycan Microarray ◽

Manual Analysis ◽

Analysis Tools ◽

Biological Polymers ◽

Informatics Tools

Glycans are one of the major biological polymers found in the mammalian body. They play a vital role in a number of physiologic and pathologic conditions. Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions. In this review, we describe the intricacies of the generation of glycan microarray data and the experimental methods for studying binding. We highlight the importance of this knowledge before moving on to the data analysis. We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics tools.

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Web-based design and analysis tools for CRISPR base editing

BMC Bioinformatics ◽

10.1186/s12859-018-2585-4 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 39

Author(s):

Gue-Ho Hwang ◽

Jeongbin Park ◽

Kayeong Lim ◽

Sunghyun Kim ◽

Jihyeon Yu ◽

...

Keyword(s):

Web Based ◽

Base Editing ◽

Analysis Tools

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SEVA 3.0: an update of the Standard European Vector Architecture for enabling portability of genetic constructs among diverse bacterial hosts

Nucleic Acids Research ◽

10.1093/nar/gkz1024 ◽

2019 ◽

Vol 48 (D1) ◽

pp. D1164-D1170 ◽

Cited By ~ 17

Author(s):

Esteban Martínez-García ◽

Angel Goñi-Moreno ◽

Bryan Bartley ◽

James McLaughlin ◽

Lucas Sánchez-Sampedro ◽

...

Keyword(s):

Synthetic Biology ◽

Bacterial Species ◽

Web Based ◽

Genomic Engineering ◽

Bioinformatic Tools ◽

Synthetic Biology Open Language ◽

User Friendly ◽

Machine Readable ◽

Genetic Constructs

Abstract The Standard European Vector Architecture 3.0 database (SEVA-DB 3.0, http://seva.cnb.csic.es) is the update of the platform launched in 2013 both as a web-based resource and as a material repository of formatted genetic tools (mostly plasmids) for analysis, construction and deployment of complex bacterial phenotypes. The period between the first version of SEVA-DB and the present time has witnessed several technical, computational and conceptual advances in genetic/genomic engineering of prokaryotes that have enabled upgrading of the utilities of the updated database. Novelties include not only a more user-friendly web interface and many more plasmid vectors, but also new links of the plasmids to advanced bioinformatic tools. These provide an intuitive visualization of the constructs at stake and a range of virtual manipulations of DNA segments that were not possible before. Finally, the list of canonical SEVA plasmids is available in machine-readable SBOL (Synthetic Biology Open Language) format. This ensures interoperability with other platforms and affords simulations of their behaviour under different in vivo conditions. We argue that the SEVA-DB will remain a useful resource for extending Synthetic Biology approaches towards non-standard bacterial species as well as genetically programming new prokaryotic chassis for a suite of fundamental and biotechnological endeavours.

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