Bioinformatics

IAP 2009: BIOBASE Knowledge Library and Explain Analysis System Training

Posted January 5th, 2009 by Ryan Gray

Biobase logo

Save time and get more out of your data. Learn how to use BIOBASE Knowledge Library (BKL), licensed by MIT Libraries. BIOBASE offers curated databases and analysis tools designed to help biomarker, systems biology and life science researchers accelerate discovery processes. Included in this product is TRANSFAC®, TRANSPATH® and PROTEOME™ products. The BKL is great for research applications including gene set enrichment analysis, functional analysis, SNP analysis, gene expression analysis, and drug discovery. Also, learn about ExPlain Analysis Systems to perform gene regulation and systems biology focused biological interpretation of high throughput experiments like microarrays, proteomic data, and ChIP-chip experiments.

WHEN: Thursday, January 22, 9am – 12pm

WHERE: DIRC, 14N-132

Enrollment is on a first-come, first-served basis and is limited to 20 participants.

Contact Courtney Crummett with any questions.

Check out the MIT Libraries’ IAP 2009 sessions!

Posted December 19th, 2008 by Ryan Gray

IAP logo 2009

Are you wondering what an RSS feed is and how it can help your research?

Want to learn more about using GIS, EndNote or RefWorks?

Need to find chemical information, social science data, or patents?

Want to learn Japanese book-binding, improve your photography, or how to compost with worms?

Look no further! Take a peek at all of the MIT Libraries IAP Activities offered in 2009.

Ensembl Training at MIT Libraries: This Friday!

Posted November 12th, 2008 by Ryan Gray
Ensembl Logo

Browsing Genses and Genomes with Ensembl.

Free software system includes automatic annotation of selected eukaryotic genomes.

WHEN: Friday, November 14, 9am – 4pm (drop-in)

WHERE: DIRC, 14N-132

Contact Courtney Crummett with questions.

The workshop will include an introduction to Ensembl, a tour of the most important Ensembl views, and an overview of how Ensembl gene and transcripts predictions are made. Participants will learn about comparative genomics and proteomics tools (orthologues, protein families, alignments) or variation tools (SNPs, haplotypes, linkage disquilibrium). The workshop also covers data mining and large data set retrieval with BioMart.

Light snacks provided.

Bioinformatics Training @ MIT Libraries

Posted October 27th, 2008 by Ryan Gray

GeneGo logo Ensembl Logo Ingenuity Logo

GeneGo Showcase
WHEN: Wednesday, November 5, 1-3 PM
WHERE: DIRC, 14N-132
GeneGo Inc will host a software demonstration and hands on training for their MetaCore pathway analysis tool.

Ensembl Training
WHEN: Friday, November 14, 9AM- 5PM
Learn how to use this free software system that includes automatic annotation of selected eukaryotic genomes.
Ingenuity Training
WHEN: Tuesday, December 2, 9AM-12PM
Learn pathways analysis tools that help researchers analyze their experimental data in the context of biological pathways and functions.
Questions? Contact Courtney Crummett.

More Bioinformatics Resources.

National Library of Medicine (NLM) Fellow Profiled by Oak Ridge Institute for Science and Education (ORISE)

Posted October 22nd, 2008 by Heather Denny

Courtney Crummett, MIT Libraries’ Bioinformatics Librarian, has been featured in a recent profile by the Oak Ridge Institute for Science and Education (ORISE), a U.S. Department of Energy institute focusing on science education and research. Her profile is featured amongst other scholars in the areas of science, mathematics, engineering, and other technical fields.

Crummett came to the MIT Libraries in 2007 as part of the highly selective National Library of Medicine (NLM) fellowship program. As part of her fellowship she was involved in a variety of challenging projects that included developing a video series of bioinformatics tutorials with Countway Library, supporting outreach efforts to HST, and working on scholarly publishing issues. In September of this year she accepted the position of Bioinformatics Librarian with MIT’s Engineering and Science Libraries. Read Crummett’s profile…

JulyAP 2008 Workshop: Bioinformatics for Beginners

Posted July 11th, 2008 by Ryan Gray

NCBI logo

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, July 18, noon – 1pm

Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

Feel free to bring your lunch! Drinks and dessert will be provided.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

Full schedule of JulyAP 2008 information workshops

Bioinformatics Video Tutorials Now Available!

Posted May 2nd, 2008 by Remlee Green

BITS header

Check out the new bioinformatics video tutorials, developed by the MIT Engineering and Science Libraries and Harvard’s Countway Library of Medicine. These tutorials aim to bring research help to your desktop.

The first installment of BITS covers the UCSC Genome Browser, which contains reference sequences and working draft assemblies for a large collection of genomes. The UCSC Genome Browser is developed and maintained by the Genome Bioinformatics Group, a cross-departmental team within the Center for Biomolecular Science and Engineering at UCSC.

Watch these videos to learn more about the UCSC Genome Browser. Learn how to retrieve DNA sequence, display and configure the annotation tracks, identify gene intron-exon boundaries, and use the BLAT tool.

BIT 1.1: UCSC Genome Browser: Getting DNA Sequence (3:57)
BIT 1.2: UCSC Genome Browser: Using Annotation Tracks (5:47)
BIT 1.3: UCSC Genome Browser: Locating Intron-Exon Boundaries (4:56)
BIT 1.4: UCSC Genome Browser: Searching with BLAT (6:14)

Learn at your own convenience and your own pace.

Find the Bioinformatics Tutorial Series (BITS), and many other tutorials, on the video tutorials page.

Questions? Email ask-bioinfo@mit.edu.

IAPril 2008: Bioinformatics for Beginners

Posted April 11th, 2008 by Ryan Gray

NCBI logo
Bioinformatics for Beginners
Amy Stout, Courtney Crummett

Learn how to find and use information more effectively in our hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

**NOTE that different events will be happening throughout the month of April and early May.**

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, April 18, 12pm (noon)

Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

IAPril Information Workshops 2008

Posted April 1st, 2008 by Ryan Gray

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Learn how to find and use information more effectively in these hands-on workshops. No advanced registration required. Light refreshments will be served at each session.

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Fridays in April (and May), 12pm (noon)

April 11: Managing your references: Overview of EndNote, RefWorks and Zotero
Remlee Green, Mathew Willmott

Using citation management software to create and maintain a collection of references is becoming more common and important in today’s academic world. This session will focus on EndNote, RefWorks, and Zotero, the three major options for bibliographic software at MIT.

April 18: Bioinformatics for Beginners
Amy Stout, Courtney Crummett

Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

April 25: EndNote Basics
Peter Cohn, Anita Perkins

EndNote is a “personal bibliographic software” package which allows you to create and manage a database of bibliographic references.

May 2: Citation Surfing: Using Databases to Track Article Citations
Michael M Noga

Have your ever used the Web of Science to find citations? Have you used Google Scholar? Perhaps you have used citation links in journal articles. This session will explore the different ways you can use citation searching to identify literature on a subject.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

IAP 2008: Bioinformatics for Beginners

Posted January 13th, 2008 by Ryan Gray

NCBI2

The National Center for Biotechnology Information (NCBI) Entrez family of databases is the foundation of knowledge for molecular level bioscience research. Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

WHEN: Thursday, January 10, 4 – 5 pm
Friday, January 18, 12:30 – 1:30 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 20 participants.

Contact Amy Stout with any questions.

IAP 2008: BIOBASE ExPlain Training

Posted January 13th, 2008 by Ryan Gray

BIOBASE

Scientists from BIOBASE will do training on these bioinformatics databases that include Proteome, TransFac, TransPath, and ExPlain, with focus on the new database ExPlain and updates on new features for all of them. The MIT Libraries subscribes to these, and you will find them on VERA. There will be a 2 hour training session plus hands-on time to work on your own research if you wish.

WHEN: Thursday, January 17, 1 – 3 pm

WHERE: 14N-132, DIRC

Enrollment is on a first-come, first-served basis and is limited to 30 participants.

Contact Louisa Worthington Rogers with any questions.

NCBI Bioinformatics Mini-Courses: November 8-9

Posted October 17th, 2007 by Remlee Green

NCBI logo

The MIT Libraries will sponsor a series of 4 NCBI bioinformatics mini-courses on, November 8-9, 2007 in the Hayden Library DIRC, 14N-132. Each course is 2.5 hours in length, including a lecture followed by a 1-hour hands-on session. There is no advance registration but space is limited. There are computers for 20 attendees, plus space for 10 attendees with their own laptops.

Contact Louisa Worthington Rogers with questions.

Thursday, November 8:

9:30am-12:00pm – Microbial Genomes Quickstart (New class!)

In this mini-course, you will learn how to access the microbial genome sequences and annotations, how to navigate through and download the gene and protein datasets, and will be introduced to the available genomic and comparative genomic analysis tools. The course will address practical discovery questions such as ‘Are there identifiable genes in microbial genomes that may be horizontally transferred?’ and ‘What are the differences between closely-related pathogenic and non-pathogenic bacteria?’

1:00pm-3:30pm – Mapviewer Quick Start

In this course, we will use the human genome Map Viewer. Used to view the NCBI assembly of the complete human genome, Map Viewer is a valuable tool for the identification and localization of genes that contribute to human disease. In this course, we will see how to view different human genome maps and make best use of them. We will learn to locate a human gene, download its sequence along with its upstream sequence (to analyze promoter regions), obtain exon-intron coordinates, find a possible splice variant and identify whether the variations in the gene are associated with a disease.

Friday, November 9:

9:30am-12:00pm – Structural Analysis Quick Start

This course covers how to visualize and annotate 3D protein structures using NCBI’s Cn3D, identify conserved domain(s) present in a protein, search for other proteins containing similar domain(s), explore a 3D modeling template for the query protein and find distant sequence homologs that may not be identified by BLAST.

1:00pm-3:30pm – Making Sense of DNA and Protein Sequences

In this mini-course, we will find a gene within a eukaryotic DNA sequence. We will then predict the function of the implied protein product by seeking sequence similarities to proteins of documented function using BLAST and other tools. Finally, we will find a 3D modeling template for this protein sequence using a Conserved Domain Database Search.

About the Instructors:

Medha Bhagwat and Steve Pechous are biologists on the User Services staff of the National Center for Biotechnology Information.

JulyAP Workshop: Bioinformatics for Beginners

Posted July 27th, 2007 by Ryan Gray

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, August 3, noon – 1pm

NCBI’s Entrez family of databases is the foundation of knowledge for molecular level bioscience research. Class attendees will learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool. The session is a hands-on practicum and an excellent starting point for people who are new to, or curious about bioinformatics research tools.

NCBI Bioinformatics

Feel free to bring your lunch! Drinks and dessert will be provided.

Sponsored by the MIT Libraries.

Contact the Science Library for more information.

Full schedule of JulyAP 2007 information workshops

NCBI Bioinformatics Mini-Courses: May 10-11

Posted April 13th, 2007 by Remlee Green

NCBI logo

The MIT Libraries will sponsor a series of 4 NCBI bioinformatics mini-courses on May 10-11, 2007 in the Hayden Library DIRC, 14N-132. Each course is 2.5 hours in length, including a lecture followed by a 1-hour hands-on session. To register, send your name, name of course(s), department, affiliation, and email address to Louisa Worthington Rogers. There is a limit of 20 attendees per course. (UPDATE: Classes are full, and no additional sign-ups will be accepted at this time.)

Thursday, May 10:

9:30-12:00 – Making Sense of DNA and Protein Sequences
In this mini-course, we will find a gene within a eukaryotic DNA sequence. We will then predict the function of the implied protein product by seeking sequence similarities to proteins of documented function using BLAST and other tools. Finally, we will find a 3D modeling template for this protein sequence using a Conserved Domain Database Search.

1:00-3:30 – Entrez Gene Quick Start
In this course, we will use NCBI ‘s Entrez Gene to learn how to obtain information about a human gene such as its mRNA and genomic sequence, gene structure (exon-intron locations), function and phenotypes associated with mutations. We will also learn how to determine whether the SNPs in the coding region of a gene are known to alter the function of the protein product.

Friday, May 11:

9:30-12:00 – Structural Analysis Quick Start
This course covers how to visualize and annotate 3D protein structures using NCBI’s Cn3D, identify conserved domain(s) present in a protein, seach for other proteins containing similar domain(s), explore a 3D modeling template for the query protein and find distant sequence homologs that may not be identified by BLAST.

1:00-3:30 – Mapviewer Quick Start
In this course, we will use the human genome Map Viewer. Used to view the NCBI assembly of the complete human genome, Map Viewer is a valuable tool for the identification and localization of genes that contribute to human disease. In this course, we will see how to view different human genome maps and make best use of them. We will learn to locate a human gene, download its sequence along with its upstream sequence (to analyze promoter regions), obtain exon-intron coordinates, find a possible splice variant and identify whether the variations in the gene are associated with a disease.

About the Instructors:

Simin Assadi and Steve Pechous are biologists on the User Services staff of the National Center for Biotechnology Information.

NOTE: CLASSES ARE FULL!

Upcoming IAPril Events!

Posted March 29th, 2007 by Ryan Gray

Learn how to find and use information more effectively in these hands-on workshops.

**NOTE that different events will be happening throughout the month of April. Click here for a complete listing of events.**

RefWorks Basics

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Wednesday, April 4, 5-6pm

RefWorks is a web-based resource designed to help you to organize references and create a bibliography. RefWorks allows you to search, retrieve relevant citations, and build your bibliography. It allows users to create individual or group accounts, and makes it easy to write papers, or post your results to web pages.

This session will be a hands-on practicum. Attendees will create a personal web account and create a database of cited literature by importing references from resources such as Barton, Web of Science, PubMed and other sources of published literature. You will learn how to organize your references, and to generate manuscripts and bibliographies.

Bioinformatics for Beginners

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Friday, April 6, 12-2pm

This class is a basic introduction to NCBI bioinformatics resources. It covers the available databases, details of sequence records, and basic BLAST searching.

No advanced registration required.

Sponsored by the MIT Libraries.
Contact the Science Library for more information.

IAPril Information Workshops 2007

Posted March 27th, 2007 by Ryan Gray

Learn how to find and use information more effectively in these hands-on workshops.

WHERE: 14N-132 (Digital Instruction Resource Center – DIRC)

WHEN: Every Wednesday in April at 5, and every Friday in April at 12pm (noon). Light refreshments will be served.

Wednesday, April 4, 5-6pm, RefWorks Basics

RefWorks is a web-based resource designed to help you to organize references and create a bibliography. RefWorks allows you to search, retrieve relevant citations, and build your bibliography. It allows users to create individual or group accounts, and makes it easy to write papers, or post your results to web pages.

This session will be a hands-on practicum. Attendees will create a personal web account and create a database of cited literature by importing references from resources such as Barton, Web of Science, PubMed and other sources of published literature. You will learn how to organize your references, and to generate manuscripts and bibliographies.

Friday, April 6, 12-2pm, Bioinformatics for Beginners

This class is a basic introduction to NCBI bioinformatics resources. It covers the available databases, details of sequence records, and basic BLAST searching.

Wednesday, April 11, 5-6pm, EndNote Basics

EndNote is a “personal bibliographic software” package which allows you to create and manage a database of bibliographic references. Your database can be used to automatically generate in-text citations and bibliographies in your manuscripts. It can also help you organize and manage your PDF files. This session will be a hands-on practicum. Attendees will create a personal database of cited literature by importing references from resources such as Barton, Web of Science, PubMed and other sources of published literature. You will learn how to search and manipulate databases, and to generate a manuscript and bibliography.

Friday, April 13, 12-1pm: Patent Searching Fundamentals

While you won’t come out of this session qualified to be a patent attorney, you will be able to successfully find patent references from all over the world and know how to obtain patent text and diagrams. The session will be a hands-on practicum which will help de-mystify the patent literature and expose attendees to key resources for finding patent literature. Using patent literature is important for understanding competitive technologies and keeping abreast of current product innovations.

Wednesday, April 18, 5-6pm: Flavors of Citation Searching

Have you ever used Web of Science to find citations? Have you used Google Scholar? Ever used citation links in journal articles? This session will explore the different ways you can use the citation searching method for identifying literature on a subject to benefit of your research. The concept of citation searching has been around for over 50 years, but it has evolved with technology. Several examples will be given, and we would enjoy hearing about your own techniques.

Friday, April 20, 12-1pm: Copyright and Scholarly Publication: Retaining Rights & Increasing the Impact of Research

Can you use and re-use your own work for future writing and teaching? Or is it locked tight behind a vault of copyright restrictions? This session will help you find the keys to fully realize the potential of your own work for yourself and the world. It will provide a very brief summary of copyright law and how it affects your work, and an overview of actions you can take to improve the impact and reach of your research – including why retaining rights to your work matters, and how you can take advantage such rights to increase citation and readership.

Wednesday, April 25, 5-6:30pm: Library toolbars, extensions and web apps: little tools with big impact

Tired of hopping between Google Scholar, Amazon, and library catalogs and databases? Can’t find that great article you meant to read later? Need better ways of sharing scholarly resources within your group?

Come hear about some new web tools that may help you work more efficiently. Learn to organize and share your references, catalog your personal book collections online, and search seamlessly between library resources and other web sites.

We will demo: LibraryThing, del.icio.us, CiteULike, library-relevant Firefox extensions, and more.

Friday, April 27, 12-1pm: Company Research for Engineers and Scientists: Know your Prospective Employer or Partner

You may be a skilled investigator in the area of Science or Engineering, but what do you know about company research? This session will introduce you to library-supported databases about companies and industries. We will also use examples and hands-on exercises to demonstrate strategies for learning about industry trends and prospective employers or partners.

No advanced registration required.

Sponsored by the MIT Libraries.
Contact the Science Library for more information.

Sign up now for the EBI Bioinformatics Roadshow on March 12 – 13

Posted February 23rd, 2007 by Remlee Green

EMBL-EBI logo

The European Bioinformatics Institute (EBI) will be teaching 5 modules from their Bioinformatics Roadshow at Whitehead Institute and MIT on March 12 and 13. Each module lasts a half day and includes a lecture and hands-on training. For more information, see the complete session descriptions.

Monday, 3/12:
9:00-12:30: Transcriptomes – Intro (Whitehead – 7th floor)
1:30-5:00: Protein Structure – Intro (MIT 14N-132)
1:30-5:00: Intro Pathway Analysis Using Reactome (Whitehead – 7th floor)

Tuesday, 3/13:
9:00-12:30: Proteomes – Intro to Public-domain Resources (MIT 14N-132)
1:30-5:00: PRIDE for Proteomic Scientists (MIT 14N-132)

The Bioinformatics Roadshow is sponsored by Whitehead Institute, the MIT Libraries, the MIT Center for Cancer Research, the MIT Integrative Cancer Biology Program, and the MIT Center for Environmental Health Sciences.

To sign up for sessions at Whitehead, contact sherrin@wi.mit.edu.
To sign up for sessions at MIT, contact: charliew@mit.edu.
Questions? Contact Louisa Worthington Rogers, the MIT Biology, Medicine & Neurosciences Librarian.

Learn about Protein Sequence Analysis tools

Posted October 20th, 2005 by mit-admin

Learn how to find information in bioinformatics in this hands-on session. Attendees should have a basic familiarity with the life sciences but limited exposure to bioinformatics. The session will consist of a 1-hour lecture followed by a 1-hour hands-on exercise.

Presented by Charlie Whittaker, Research Scientist, MIT Center for Cancer Research.

Introduction to Protein Sequence Analysis
Thursday, November 17: 1-3pm
14N-132: Digital Instruction Resource Center

Learn how to obtain protein sequences from a variety of sources, perform multiple alignments, phylogenetic analysis and domain/motif analysis. In addition, instruction on obtaining and interpreting gene ontology annotations will be provided.

Advance registration is required. Please register by emailing elworthi@mit.edu.

Sponsored by the MIT Science Library.

Also recommended: Introduction to Genome Sequence Analysis – November 15, 1-3pm

Learn about Genome Sequence Analysis tools

Posted October 20th, 2005 by mit-admin

Learn how to find information in bioinformatics in this hands-on session. Attendees should have a basic familiarity with the life sciences but limited exposure to bioinformatics. The session will consist of a 1-hour lecture followed by a 1-hour hands-on exercise.

Presented by Charlie Whittaker, Research Scientist, MIT Center for Cancer Research.

Introduction to Genome Sequence Analysis
Tuesday, November 15: 1-3pm
14N-132: Digital Instruction Resource Center

Become familiar with accessing, visualizing and interpreting genomic data. The UCSC genome database and browser will be used to perform sequence, text and coordinate-based queries. View and interpret the results and download the data for use in other applications. In addition, an introduction to other useful genomics resources (Ensembl, NCBI and JGI) will be provided.

Advanced registration is required. Please register by emailing elworthi@mit.edu.

Sponsored by the MIT Science Library.

Also recommended: Introduction to Protein Sequence Analysis – November 17, 1-3pm