Biomedical Sciences Graduate Students

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Key Resources and Tools

Selected Resources to Find Books, Articles, and Protocols

Find Print and Online Books

Virgo UVA’s Library Catalog - search for print or online books at any of UVA's libraries (choose Limit by Resource Type Books after searching)

Find Article Citations and Preprints

PubMed
- PubMed toolkit (we recommend the Handouts and the Quick Tours)
Web of Science
medRxiv (health sciences preprints)
bioRxiv (biology preprints)

Search full-text articles by collection

PubMed Central (PMC) (collection of publications resulting from NIH funding)
Europe PMC (worldwide collection of life science publications and preprints and repository for many international funders)

Search full-text articles by publisher

Clinical Key (Elsevier)
LWW Total Access (Lippincott)
ScienceDirect (Elsevier)
SpringerLINK
Wiley Online Library

Find Protocols and Other Resources

Current Protocols
- See our full guide on Finding Protocols
BenchSci - Search Antibodies - Use the free version of BenchSci for individuals

Off-Grounds Access

U VA Anywhere: Provides an off-Grounds connection via VPN software to library resources (databases, e-journals, e-books etc) that normally require you to be on Grounds to use them.
Interlibrary Loan: request copies of books or journal articles UVA doesn't own (UVA-only; login required)

Research Data and Computing

Free Expert Consultations

Research @ HSL - Expert assistance with biomedical literature search and data discovery, organizing and managing your research project and bibliography, creating presentations and posters, and disseminating and sharing your research.
Data @ HSL - Data consultation services and biomedical data and statistics training opportunities. Get expert consultations by appointment on statistical software such as R, python, Stata, SAS, and SPSS
PHS @ the Library - Free consultation service to address introductory statistics and research methods questions.
UVA Research Computing - help with cutting-edge computational resources and issues around optimization, parallelization, workflow, etc.

Software at UVA

U VA Software Gateway: list of licensed software provided by UVa

Online Learning

Online courses through UVA's subscription to LinkedIn Learning (formerly Lynda.com)
E-books through O'Reilly

Presenting and Publishing

Citation Management

Our Citation Management Guide

Writing and Teaching Resources

Theses & Dissertations

Libra: UVA's electronic dissertations and master's theses repository. Also contains other UVA scholarly works and datasets.

Posters and Presentations

Our guide to creating a poster in PowerPoint, including links to UVa logos

Types of Literature

How can you distinguish Primary, Secondary and Tertiary information?

Primary Scientific Literature

Original information/materials on which research is based on and it is usually published in a peer-review journal. It includes original research, dissertations, technical reports, conference papers, and patents. It may also include data sets, pre-prints or preliminary reports.

Case Study: Reading a Primary Research Article from a Journal

How to locate primary literature?

Begin your search in a subject-specific database such as PubMed, or choose one from the A-Z Databases .
Perform your search on a topic.
Once you have a set of search results, look for articles where the author has conducted original research. A primary research article will include: a ) an introduction with a statement of the research objective, b) a methods section that details exactly how the research was performed, with enough information that another researcher could replicate it, a c) results section that describes the data collected, including charts or graphs and statistical analysis, and a d) discussion section that interprets the results within the context of the research objective

Secondary Literature

Secondary sources of information are based on primary sources. They describe, interpret, analyze and evaluate primary sources of information.

Examples of secondary sources include:

review articles or analysis of research studies about the same topic (also often in peer-reviewed publications), systematic reviews.
biographies, reviews, or critiques of an author

How to locate Secondary Literature?

From the Library's homepage, begin your search in Virgo or select a subject-specific database from the A-Z Databases . Example databases could be PubMed, Web of Science, etc.
Use the filters (PubMed) or Refine (Web of Science) to publication types such as Reviews, or Systematic reviews or Meta-analysis.

Tertiary Literature

Tertiary literature synthesizes information from primary and secondary literature. Tertiary literature can include books, textbooks, encyclopedias, and dictionaries.

How to locate Tertiary Literature?

From the Library's homepage, begin your search in Virgo
Limit by Resource Type Books.

Journal Club Tips

Preparing for Journal Club

How to Give a Good Journal Club Presentation (from UVA Pharmacology)

Paper Selection
Step 1: pick a good paper. What makes a "good" Journal Club paper? Papers that present an important concept in a clear manner. Many excellent papers are published but the data does not lend itself well to a clear presentation. Overall features:

should clearly state WHY doing the problem in the first place (significance) – find in the introduction, should be well referenced, shouldn't have to go to additional sources unless need to check specifics.
should clearly state WHAT is the problem to be solved – see the introduction.
should clearly state HOW the problem is to be solved – see Experimental Procedures.
should clearly state the CONCLUSIONS of the paper – see Discussion.

If you have been assigned a mentor for the journal club, consult the mentor at least 2 weeks in advance and choose a paper that is interesting to your mentor. Before you prepare your journal club presentation, read a good recent review on the topic.

General Presentation Tips
Never Assume...

Never assume the audience understands the technique – always explain how each experiment is done and the limitations of the technique.
Never assume the audience is thinking – always explain what question the experiment is going to answer, explain the conclusion of each experiment, the limits of interpretation and if the experiment answers the question.
Never assume the audience is listening – at the end of your presentation, again present the problem or question, the minimum relevant pieces of data that answered the question, the conclusion and if the data supports the conclusion.
If the paper focuses on a specific protein, it is important to look up some basic aspects of this protein family. You will invariably get questions about the functional domains, orthologs, and homologs.

Make figures large enough to read. Re-label if necessary.

Organizational Tips
Identify the problem and place it in the scientific context

Present overall model that is being addressed and identify which part of the model the paper you are going to present is addressing (in other words, you are presenting the introduction to the paper even before you tell them what paper you are going to be presenting).
Present background, but only enough so that audience can understand the question
Identify the paper title, authors and Journal.
Present only relevant data that supports model and present that data thoroughly.
You do not need to present every experiment in a paper. Once again, majority of the experiments are controls, you need to know how to identify the controls and present them as data that supports the relevant data. Eliminate any obviously redundant or irrelevant experiments.
If paper being presented is using a number of mutants, rename mutants so that they are easier to remember, color code them so they are easier to remember.

Take Home Message!
At the end of Journal Club everyone in the room should be able to answer three simple questions:

What was the question the authors were trying to answer?
What was the most significant piece of data the authors presented to answer the question?
Did the data conclusively answer the authors’ question?

If they can, you have given a good Journal Club.

Figure Presentation Tips
Only present one experiment/slide. Make sure that the figure is LARGE enough to be seen from the back of the room. When you present the relevant data, remember:

to have all parts of the figured labeled clearly (use color)
Define abbreviations, and avoid too much jargon
to state what technique is being used
to explain clearly what this technique measures
to clearly explain the results
AND, last but not least, explain how the experiment answers the overall question, what limits there are on the interpretation of the result and how any limits were addressed in the paper (additional experiments, controls, etc.)

Some psychological aspects for those who will be presenting for the first time to the department
Presenting these journal clubs can be a stressful experience – especially if this is your first presentation to the entire department. There are a few things to keep in mind.

The attending faculty members are not there to judge you – they are there because they find the paper or the topic interesting.
You are not expected to be an expert in this area but you are expected to put in a sincere and determined effort.
When you are confronted with critical comments about the paper, don’t take it personally. It is not your work – you are merely presenting it.
An active discussion (including criticisms about the results and conclusions) means that the audience is engaged and you are doing your job.
You should feel free to play the devil’s advocate and defend the authors but you are not obliged to.
If you feel extremely nervous before the presentation, take a moment and tell the audience that you are nervous and it will take a few minutes before you settle down

Other Resources

Biomedical Science

Related Content

Workshops