Help for basic science researchers

Working on basic science research? Pitt’s libraries have specialized services and resources available to the University’s large population of faculty, postdoc, staff, and graduate and undergraduate researchers in the basic sciences.

Animal research
Among its many areas of oversight, the Pitt institutional animal care and use committee (IACUC) ensures that researchers are compliant with the Department of Agriculture Animal Welfare Act, including USDA policy 12. This policy requires that investigators consider alternatives to procedures that may cause more than momentary or slight pain or distress to research animals. The USDA considers the performance of database searches and analysis of articles an effective method for demonstrating compliance with this requirement. Sample literature searches can be found on the IACUC policy web page. Literature searches and corresponding narratives should address the following “3Rs”:

• Reduction — Minimize the number of animals used, without jeopardizing statistical validity.

• Refinement — Employ techniques that reduce pain and distress.

• Replacement — Substitute animals with non-animal methods (i.e., computer simulation) or lower animal species.

The Pitt libraries provide access to many databases that can be used to complete an IACUC literature search: Agricola, BIOSIS Previews, EMBASE, PubMed and Web of Science. The Health Sciences Library System (HSLS) also has an IACUC liaison librarian who can assist with searching the literature for animal alternatives.

Data analysis
Since 2002, the HSLS Molecular Biology Information Service (MBIS) has taken a four-pronged approach to helping biomedical researchers. We provide:

• a web portal with information about services, classes and accessing bioinformatics resources and tools;

• bioinformatics consultations with researchers at all levels;

• educational outreach including hands-on workshops, lectures in graduate and undergraduate classes, and talks in departmental seminars and conferences highlighting the use of bioinformatics tools in solving real-life scientific problems; and

• licensing of commercial software to assist researchers with analyzing and interpreting their data, as well as saving them the expense of purchasing and managing individual licenses.

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Below is a typical research experimental workflow and the recommended tools for each step. You can register for the licensed software at http://hsls.libguides.com/molbio/licensedtools/resources.

• Information gathering: Resources are useful for locating supporting evidence to guide subsequent steps in the research process. The last four were developed by HSLS.

— BIOBASE databases cover human inherited disease mutations (HGMD), pharmacogenomics mutations (PGMD), interlinked reports on genes, diseases, drugs and pathways (PROTEOME), and data on eukaryotic transcription factors, their genomic binding sites and DNA-binding profiles (TRANSFAC/MATCH).

— Correlation Engine identifies mechanisms of disease, drug targets and prognostic/predictive biomarkers.

—F1000 Workspace helps researchers discover, read, annotate, write and share scientific research.

— InfoBoosters connect digital text to databases and retrieve relevant information on demand.

— OBRC provides quick access to major bioinformatics databases, software tools and related literature on the web.

— Search.bioPreprint searches preprint databases to discover cutting edge, yet-to-be published or reviewed biomedical research articles.

— Search.HSLS.MolBio provides a federated search of molecular biology databases, tools, protocols, videos and recommended articles.

• Sequence manipulation: Molecular biology software packages for viewing, editing, analyzing and managing nucleotide and amino acid sequence data.

— CLC Main Workbench analyzes DNA, RNA and protein sequence data.

— Lasergene focuses on molecular biology and structural biology tools.

— Sequencher offers Sanger or Next-Generation Sequencing (NGS) DNA sequence analysis and RNA-seq or microarray data analysis.

— Vector NTI contains a comprehensive set of sequence data analysis and management tools.

• Transcriptomics: Bioinformatics software suites for analyzing and visualizing gene expression data derived from microarray or NGS-driven RNA-seq experiments.

—Biomedical Genomics Workbench helps with analysis of cancer and hereditary disease NGS data generated from experiments carried out on humans, mice or rats.

— CLC Genomics Workbench supports a wide range of NGS bioinformatics applications.

— GeneSpring provides statistical tools for data analysis and visualization, including transcriptomics, genomics, metabolomics, proteomics and NGS data.

— Partek Genomics Suite guides microarray and NGS workflows.

• Genomics: Bioinformatics software for analyzing, visualizing and interpreting NGS data coming from DNA resequencing, microbiome sequencing, transcription factor ChIP-seq and bisulfite-sequencing experiments.

— Biomedical Genomics Workbench.

— CLC Genomics Workbench.

• Variant analysis: Software for detecting disease-causing genetic variants.

— Biomedical Genomics Workbench.

— CLC Genomics Workbench.

— Ingenuity Variant Analysis quickly identifies disease-causing variants.

• Pathway analysis & protein Interactions: web-based software solutions for functionally interpreting omics data.

— Correlation Engine.

— ePath3D creates publication-ready diagrams.

— Ingenuity Pathway Analysis assists with pathway analysis, predictive causal analytics and NGS/RNA-seq data analysis.

— Key Pathway Advisor interprets gene expression data.

— MetaCore provides a comprehensive systems biology analysis suite for protein interactions and disease associations.

Carrie L. Iwema is the molecular bioinformationist for the Health Sciences Library System.