Bioinformatics

Food for Thought study breaks — May 12 & 14

Posted May 11th, 2009 by mit-admin

Need a break from your studies?

Enjoy free drinks & snacks at our two Food for Thought events this week:

  • Barker Library (10-500) lobby, Tuesday May 12th, 2:30-4pm
  • Hayden Library (14S-100) lobby, Thursday May 14th, 2:30-4pm

IAPril 2009: Bioinformatics for Beginners

Posted April 6th, 2009 by Ryan Gray

bioinformatics
Learn how to find and use information more effectively in our hands-on workshops. No advanced registration required.

**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 10, 12 – 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.

Contact Howard Silver for more information.

Check out the full listing of IAPril 2009 Libraries events!

IAPril Information Workshops 2009

Posted March 27th, 2009 by Ryan Gray

Peter DIRC
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)

Endnote Basics
Friday, April 3rd, 12 – 1pm

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

Researching Companies for the Job Hunt
Thursday, April 9, 3-4:30pm

The MIT Libraries subscribe to a number of databases that you can use to research companies and industries. Using these databases, you can:
-Target companies by industry and geography
-Conduct comprehensive company and industry research
We will discuss why this type of research is critical to the job and internship search process, and how to use these databases effectively.

Contact: Anita Perkins

Bioinformatics for Beginners
Friday, April 10th, 12 – 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.
Contact: Howard Silver

Biotechnology Patent Fundamentals and Searching
Thursday, April 16, 12-1:30pm

Come and hear attorney Sonia Guterman of Lawson & Wetzen discuss the distinctive aspects of patents that make them valuable, the role of patents in capital development, along with issues surrounding filing biotech patents. She will be assisted by Drew Lowery, who received his Ph.D. in Biochemistry from MIT and is a member of Global Prior Art’s Life Science Team. Drew will discuss and demonstrate alternative ways to search biotech patent art and their suitability. At the end of the talk attendees will have the opportunity to do hands on searching.

Contact: J. Darcy Duke

Managing Research Data 101
Thursday, April 23, 12-1pm

For researchers struggling to manage their data, basic strategies will be provided for
• best practices for retention and archiving
• effective directory structures and naming conventions
• good file formats for long-term access
• data security and backup options
• metadata, tagging, and citation
• other relevant issues

Contact: MacKenzie Smith

Introduction to Market Research Databases at MIT
Friday, May 1, 12-1pm

Market research abounds on the web, but usually with a hefty price tag. This session will familiarize participants with market research accessible through MIT. We will cover types of resources available, how to navigate them, and some basic tips for using these resources.

Contact: Maggie Bartley

Check out the full listing of IAPril 2009 Libraries events!

New Installment of the BioInformatics Tutorials Series (BITS)

Posted February 23rd, 2009 by Ryan Gray

bioinformatics
New installment of the BioInformatics Tutorials Series (BITS) brought to you by MIT Engineering and Science Libraries and Harvard’s Countway Library of Medicine!

BIT 3.1: Entrez Gene (5:35)
BIT 3.2: OMIM and OMIA (6:34)
BIT 3.3: HomoloGene (6:28)

Be sure to check out our complete listing of MIT Libraries video tutorials.

MIT Libraries has Access to New Bioinformatics Tool: GeneGo MetaCore

Posted February 12th, 2009 by Ryan Gray

GeneGo MetaCore logo

GeneGo MetaCore is an integrated software suite for functional analysis of experimental data in systems biology.

You need to first register with GeneGo to access MIT’s License to MetaCore.

Don’t worry, it is fast and easy. Go to the GeneGo Resource Guide for registration information and to learn more about GeneGo MetaCore.

Login information will be sent to you ASAP (within 24hrs, M-F) and you may then login to GeneGo MetaCore.

We have training coming up on March 11th, 2009 from 9-12 Noon in the DIRC (14N-132).

Email Courtney Crummett to register.

IAP 2009: All Events for Week Ending Friday, January 30

Posted January 23rd, 2009 by Ryan Gray

IAP logo 2009

Check out all of the MIT Libraries IAP events for the week covering Monday, January 26 through Friday, January 30. A complete listing for all of IAP is also available.

Practically Genomic

Introduction to Google Maps API

Using Elevation Data and Hydrographic Tools in a GIS

QUOSA Information Manager Demo: Retrieve and Organize Article PDFs

Going Beyond Google Scholar: Using the Web of Science and other citation searching resources to discover articles

Compost with Worms…in Your Apartment!!

Mapping and Using US Census Data

Fiddle-dee-dee during IAP

Managing Research Data 101

EndNote Basics

IAP @ Humanities Library Film Series: Special Effects at the Movies

Finding & Using Historical Newspapers

Model Builder

Biotechnology Patent Fundamentals and Searching

Make your Paper File Cabinets Searchable: How to Manage Paper and Electronic Documents Effectively

RefWorks Basics

Please note that some sessions have limited availability or may require advance sign-up requirements. If you have further questions, please see individual listings for appropriate contact information.

IAP 2009: All Events for Week Ending Friday, January 23

Posted January 15th, 2009 by Ryan Gray

IAP logo 2009

Check out all of the MIT Libraries IAP events for the week covering Monday, January 19 through Friday, January 23. A complete listing for all of IAP is also available.

Patent Searching Fundamentals

Introduction to GIS Using ESRI ArcGIS Desktop

Bioinformatics for Beginners

Using NCBI’s BLAST

Organic? All-natural? Grass-fed? What Does It All MEAN??

Tips and Tricks for Keeping Up With Information: Mechanical Engineering

Open Source and Free Mapping Tools

Managing Your References: Overview of EndNote, RefWorks and Zotero

BIOBASE ExPlain Training

RefWorks Basics

Patent Searching Fundamentals

Going Beyond Google Scholar: Using the Web of Science and Other Citation Searching Resources to Discover Articles

Introduction to GIS Using Free Software Tools and Data

Career Research: Targeting and Researching Employers

Site Selection – Making Spatial Decisions Using a GIS

EndNote Basics

Please note that some sessions have limited availability or may require advance sign-up requirements. If you have further questions, please see individual listings for appropriate contact information.

IAP 2009: All Events for Week Ending Friday, January 16

Posted January 8th, 2009 by Ryan Gray

IAP logo 2009

Check out all of the MIT Libraries IAP events for the week covering Monday, January 12 through Friday, January 16. A complete listing for all of IAP is also available.

Managing Your References: Overview of EndNote, RefWorks and Zotero

Tips and Tricks for Keeping Up With Information: Materials Science & Engineering

Japanese bookbinding

EndNote Basics

Finding Research Datasets: ICPSR and the Harvard-MIT Data Center

Bioinformatics for Beginners

Managing Research Data 101

Introduction to Company and Industry Research for Engineers and Scientists

Basics of Obtaining a Patent

RefWorks Basics

Introduction to SciFinder on the Web

Humanities and Music Library Bookmobile

Keeping Current: Using RSS Feeds to Stay Ahead in Your Research

Please note that some sessions have limited availability or may require advance sign-up requirements. If you have further questions, please see individual listings for appropriate contact information.

IAP 2009: Personalized Data and Knowledge Management Series

Posted January 7th, 2009 by Ryan Gray

Researchers and students at MIT enjoy access to vast amounts of information from a variety of sources and in a variety of formats. Finding, manipulating, organizing and managing the fire-hose quantity of content that comes across your desktop can be a challenge. While we can’t offer you a ‘magic bullet’ solution for this challenge, the MIT Libraries are sponsoring a series of IAP sessions that showcase tools, training and techniques that can help you both find sources for data and to become better custodians of your own content. These sessions are organized into sub-thematic groups and are offered throughout the month. Contact the individual session sponsors if you have any questions.

CITATION MANAGEMENT

DATA, DOCUMENT AND IMAGE MANAGEMENT

BIOINFORMATICS

Think on it!
GIS

Please note that some sessions have limited availability or may require advance sign-up requirements. If you have further questions, please see individual listings for appropriate contact information.

Also browse the entire gamut of offerings by the MIT Libraries.

IAP 2009: Using NCBI’s BLAST

Posted January 6th, 2009 by Ryan Gray

NCBI logo
Want to know more about how BLAST works and how to use it more effectively in your research? Then this class is for you! This class will follow up on Bioinformatics for Beginners and lead into Advanced Bioinformatics, although attendance at the other sessions is not necessary.

WHEN:
Wednesday, January 21, 11 – 12am

WHERE:
DIRC, 14N-132

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

Contact Courtney Crummett with questions.

IAP 2009: Practically Genomic

Posted January 5th, 2009 by Ryan Gray

UCSC data

Genomics, microarrays, and massively parallel applications such as next generation sequencing have made biology research a highly quantitative field. As a result, many biologists face the challenge of mastering computers and computational methods. Our sessions are designed to begin the process.

We will provide an overview of some of the bioinformatics tools and methods mandated by modern biological research. Practical examples will be used to introduce powerful aspects of the Unix operating system, Perl, R, Excel and MySQL. We will also instruct attendees on the usage of bioinformatics tools for genomics, phylogenetics and microarray data analysis. Topics to be covered include the UCSC genome browser, GALAXY, Argo, GenePattern, Bioconductor, ClustalX, and a variety of functional annotation methods.

WHEN:
Monday, January 26, 11am – 1pm
Wednesday, January 28, 11am – 1pm
Friday, January 30, 11am – 1pm

WHERE: DIRC, 14N-132

Enrollment is on a first-come, first-served basis and is limited to 20 participants. It is requested that participants attend all sessions.

Contact Charlie Whittaker or Courtney Crummett with questions.

IAP 2009: Bioinformatics for Beginners

Posted January 5th, 2009 by Ryan Gray

bioinformatics

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:
Wednesday, January 14, 4 – 5pm
Tuesday, January 20, 5 – 6pm

WHERE: DIRC, 14N-132

Contact Howard Silver with any questions.

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

banner_logos2.jpg

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