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Explore gene-expression datasets with the Omics Dashboard

The advent of omics technologies has fostered the generation of a flood of complex, high-resolution datasets, the analysis of which remains a major hurdle and requires conversion into actionable biological knowledge. To address this challenge, Peter Karp and his colleagues from the SRI Bioinformatics Research Group have developed the Omics Dashboard within the BioCyc.org website. Here, they present their tool and its main features. The Omics Dashboard The Dashboard provides a multi-level visual read out of an expression dataset, from the cellular level to the gene level.  The user can probe their data in a fast and intuitive manner to gain a deep understanding of the data at multiple biological levels.   At the highest echelon (Figure 1) the Dashboard provides …

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Search and find olive oil compounds with OliveNet

Olive oil is now widely recognized as a key component of the health benefits provided by the “Mediterranean diet”. However, the exact composition and biological activity of olive oil and its compounds are still being investigated. OliveNet aims at gathering all information on olive oil compounds in a knowledgebase. Here, they briefly present their database and its features.   The benefits of olive oil   The health benefits of a Mediterranean diet rich in extra-virgin olive oil was illustrated by the classical Ancel Keys Seven Countries Study and more recently the methodical, multicentre Prevention with Mediterranean (PREDIMED), trial in Spain. In the context of health benefits the initial focus was on the major mono- and poly-unsaturated fatty acids, and accumulated …

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MEDLINE queries made easy with the MEDOC tool

MEDOC (MEdline DOwnloading Contrivance) is a Python program designed to download data from MEDLINE on an FTP and to load all extracted information into a local MySQL database, thus making MEDLINE search easy. MEDLINE, the biomedical data keeper Since MEDLINE’s database has been released almost 50 years ago, the number of indexed publications rose from 1 million in 1970 to 27 millions this year. The aim of this repository is to facilitate the access to the scientific literature for everyone. The NIH (National Institute of Health, USA) also provides a powerful search engine, which allows to query this database throught the well-know web interface PubMed. This search engine supports complex queries by using logical operators (OR, AND) and indexes different text …

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Best bioinformatics software for gene clustering

  Clustering is a fundamental step in the analysis of biological and omics data. It is used to construct groups of objects (genes, proteins) with related function, expression patterns, or known to interact together. In microarrays or RNA-seq experiments, gene clustering is often associated with heatmap representation for data visualization.   Choosing the right clustering tool for your analysis   Many clustering methods and algorithms have been developed and are classified into partitioning (k-means), hierarchical (connectivity-based), density-based, model-based and graph-based approaches. To help you choose between all the existing clustering tools, we asked OMICtools community to choose the best software. Here are the top 3 tools, chosen by 23 voters.   1. ClustEval 2. Babelomics 3. Altanalyze First place for …

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Best bioinformatics software for venn diagram

Venn diagrams are very simple, yet incredibly useful tools used to show all logical relations between finite collections of different sets of data. In Venn diagrams, sets of data are often represented as overlapping circles. Data that are shared between two different sets will reside at the intersection, while unique data remain outside the intersection. Venn diagrams in biology In biology and omics, Venn diagrams can be used for a variety of purposes, such as the comparison of different lists of genes or proteins (generally 2 or 3) to identify similarities and represent them in two dimensions. Most softwares allow easy extraction of the data, and let you customize the diagrams.   Continuing our series of data visualization tools, OMICtools …

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CircRNAs in human and mouse tissues

Leng Han and Chunjiang He are the creators of the tissue-specific circular RNA (circRNA) database TSCD. They performed the first global analysis of tissue-specific circRNAs and collected these data in a comprehensive database. Here, they talk about their work and how the TSCD database can help researchers explore their RNA sequencing data. A repository of more than 300,000 tissue-specific RNAs With circRNAs attracting more attention in transcriptome research, we explored the global features of tissue-specific circRNAs in embryo development and organ differentiation. To identify tissue specific circRNAs, 3 algorithms, CIRI, circRNA_finder and find_circ, were applied to RNA-seq data collected from the ENCODE project and the NCBI GEO database.   Based on the major types of circRNA, we identified more than 300,000 tissue-specific circRNAs in different tissues. Our …

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Evaluating biomedical data production with text mining

Estimating biomedical data Evaluating the impact of a scientific study is a difficult and controversial task. Recognition of the value of a biomedical study is widely measured by traditional bibliographic metrics such as the number of citations of the paper and the impact factor of the journal. However a more relevant critical success criteria for a research study likely lies in the production itself of biological data, both in terms of quality and also how these datasets can be reused to validate (or reject!) hypotheses and support new research projects. Although biological data can be deposited in specific repositories such as the GEO database, ImmPort, ENA, etc., most data are primarily disseminated in articles within the text, figures and tables. This raises the …

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