Research & Collaboration Tools

The Indiana CTSI offers a range of technologies to help its investigators better collaborate and carry out their translational research by facilitating the easy sharing of information. The following is a (growing) list of tools available to investigators through this site as well as externally. For more information or to see examples, click on the tool title.

Search & Discovery

  1. Contextual Site Search: An advanced keyword search which enables mining this site for member profiles, service cores, events, knowledge base, tags, etc., as well as external sources such as PubMed and clinical trials results.
  2. Semantic Site Search: An advanced, biomedical ontology (for instance Medical Subject Headings (MeSH) and Systematized Nomenclature of Medicine (SNOMED)--Clinical Terms) based search.
  3. Direct2Experts: Direct2Experts is a search tool which provides easy online access to profile information on faculty researchers across the country. The Indiana CTSI is one of 29 institutions in the CTSA Consortium participating in the program.
  4. GLAD4U: GLAD4U is a free, web-based tool to help researchers answer such questions as “Which genes are related to breast cancer?” GLAD4U (Gene List Automatically Derived for You) automates the process of creating gene lists. It makes use of the Entrez Programming Utilities of the National Center for Biotechnology Information (NCBI), a division of NLM.
  5. NLMplus: NLMplus is a semantic search and knowledge discovery application that simultaneously searches 59 NLM databases to allow users to discover NLM’s rich content offerings in all areas of biomedicine and health.
  6. Quertle: Quertle is an innovative website for searching and investigating the biomedical literature. It is geared to active life science professionals, including researchers and health care providers, and is designed to save them considerable time and effort in finding the literature they need. Quertle simultaneously searches multiple sources of life science literature, including the National Library of Medicine’s MEDLINE and TOXLINE.
  7. KNALIJ: KNALIJ, pronounced knowledge, helps researchers, students and health consumers visualize large amounts of data such as the information in NLM's repository PubMed. KNALIJ is a visualization tool built around the idea that the best pattern recognition system is a person’s own visual system. Presenting information in the form of visual, interactive maps can significantly improve researchers’ abilities to scan large amounts of information and dramatically reduce their time to discovery.

Collaboration

  1. Alfresco Share: Alfresco Share is an online collaboration and data sharing tool. Includes safe, fast, and secure large file sharing. For more information, see the FAQ.
  2. Research Data Sharing: See REDCap below.
  3. Discussion forums: Investigators may request assistance from the Indiana CTSI in setting up discussion forums related to their research projects, such as a lab or larger research group.
  4. SciVal: This program enables researchers to find scientists who are conducting research in similar areas, or have useful complementary expertise, whether at the IU School of Medicine or other universities that participate in SciVal.

Data Capture & Management

  1. REDCap (Research Electronic Data CAPture): REDCap is an easy-to-use database management tool used to capture, use, and share research data. It is also a tool to create, conduct, and manage online surveys.

Research Storage

  1. Research File System (RFS): RFS (based on OpenAFS) is a HIPAA-aligned system that gives researchers access to their files from a broad range of locations and enable group collaboration through file sharing.
  2. Scholarly Data Archive: The SDA Service is a HIPAA-aligned distributed storage service offered by Indiana University to faculty, staff, and graduate students who need large scale archival or near-line data storage, arranged in large files, for their research projects.

Online Surveys/Forms

  1. Surveys: The Indiana CTSI will provide assistance setting up online REDCap surveys related to research projects, ranging from simple forms to extensive, in-depth questionnaires.
  2. Electronic forms: The Indiana CTSI will assist investigators in converting paper forms used in their current research workflow into an electronic format, including developing online submissions, automated email notification (i.e.: results sent to the form processor and submitter), and a persistent, regular backed up, online database to store and review the results online. This service also includes assistance developing new online forms.

Bridging Research & Industry

  1. i2iConnect: i2iConnect is a searchable database of potential industry partners aimed at researchers and innovators looking for collaborators to take their research to the next level.

Analysis

  1. Thomson Reuters Services: Thomson Reuters Services include access to MetaCoreTM, a pathway analysis suite; MetaDrugTM, small molecule analysis tool; and Eureka, a data-mining tool. Access is provided to investigators at Indiana, Purdue and Notre Dame universities at a significantly reduced rate through a CTSI Thomson Reuters agreement.

Computational Tools

  1. Tools on IU's Supercomputers: A large number of computational biology/bioinformatics tools are available on IU's high performance supercomputers. These include programs such as: BLAST, ClustalW, FASTA, IMPUTE, MACH, MEME, MIGRATE, MPI-HMMER, MrBayes, MULTICLUSTAL, PAUP, PHYLIP, Phrap, PLINK, RepeatMasker, and TREE-PUZZLE.

Biomedical Databases

  1. GOBIOM Biomarkers Database: GOBIOM is a comprehensive collection of all clinically evaluated biomarkers associated with different therapeutic areas reported in global clinical trials and preclinical markers in patients. Access is free investigators at IU, Purdue and Notre Dame and is supported by the Indiana CTSI Bioinformatics CORE and Indiana Institute for Personalized Medicine.

Tools for Mobile Platforms

  1. iAnatomy: iAnatomy is an electronic anatomy atlas available for the iPhone and iPod touch. The app enables people to learn anatomy interactively with the ability to zoom in on images for more detail. iAnatomy used data from the National Library of Medicine’s Visible Human Project. iAnatomy was developed by Anouk Stein, M.D., a radiologist and computer programmer in Phoenix.
  2. Molecules: Molecules is an iPhone, iPodTouch, and iPad application that provides 3-D molecular modeling. Molecules has a touch-based interface and uses information from NCBI’s Entrez and PubChem databases.
  3. ORKOV: ORKOV is an iPhone and Android application that provides access to PubMed.gov. Orkov is a Greek term that refers to the Hippocratic Oath.


  4. For more information on these tools, as well as other useful topics, visit the Indiana CTSI Knowledge Base.

    If you have questions or are interested in using one or more of these tools, please contact This e-mail address is being protected from spambots. You need JavaScript enabled to view it

    

 


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