Search for newly identified gene lesions to determine whether or not they are novel; search by gene to get an overview of the known mutational spectrum for that gene; and search for a type of mutation in a specific location.

HGMD is integrated with other bioscience resources such as OMIM, Entrez Gene and the Human Gene Nomenclature Committee. The free version of HGMD only contains 3 year old data while the licensed version contains current data and a better search interface, so take advantage of this great resource!

To access HGMD, search for “HGMD” in MIT Libraries’ Vera. Click on “BIOBASE Knowledge Library-ExPlain and HGMD” and then “HGMD.”

Contact Courtney Crummett with any questions.

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

WHEN: Thursday, July 9, 1pm – 2pm

Learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool.

Contact Howard Silver with any questions.

Full schedule of JulyAP 2009 workshops

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

WHEN: Wednesday, July 8, 9am – 12pm

Learn how to use this gene expression tool licensed by MIT Libraries. Bring data!

Contact Courtney Crummett with any questions.

Full schedule of JulyAP 2009 workshops

All Broad employees can use the new Broad Library for library services. Dave Richardson (617.714.7902), the Broad Librarian, can answer questions related to this transition. The Broad institute also has more information available on their intranet for employees.

All workshops will take place in the Digital Instruction Resource Center (DIRC), 14N-132.

GeneGo Training
Wednesday, July 8, 9am – 12pm
Learn how to use this gene expression tool licensed by MIT Libraries. Bring data!
Contact: Courtney Crummett

Bioinformatics for Beginners
Thursday, July 9, 1pm – 2pm
Learn about the organization of key NCBI databases, understand the database record structure, and work with the BLAST search tool.
Contact: Howard Silver

EndNote Basics
Friday, July 10, 12pm – 1pm
Endnote is a “personal bibliographic software” package which allows you to create and manage a database of bibliographic references. Learn how to find and use information more effectively in our hands-on workshops.
Contact: Peter Cohn

OAG as a Travel Planner Tool
Monday, July 13, 12pm – 1pm
OAG Travel Planner Pro is the premier customizable online tool for business and professional travelers who need to make and manage complex travel plans.
Contact: Barbara Williams

RefWorks Basics
Friday, July 17, 12pm – 1pm
RefWorks is a web-based resource designed to help you organize references and create a bibliography. RefWorks allows you to search, retrieve relevant citations, easily cite references as you write your paper, and build your bibliography. It allows users to create individual or group accounts.
Contact: Anita Perkins

Accessing the Aero/Astro Collection
Monday, July 6 and Monday, July 20, 12pm – 1pm
Find out where Aero/Astro materials are now located. This session will highlight the various Aero/Astro collections and how to access them.
This session is limited to 25 participants. To register, contact Barbara Williams.

Sequence Alignment
Wednesday, July 22, 10am – 12pm
Explore sequence alignment algorithms and their practical applications. Session will include a hands-on algorithm exercise and practical usage information (Clustal, BLAST, BLAT, Maq).
Contact: Charlie Whittaker

DSpace@MIT for Research Collections
Friday, July 24 and Monday, July 27, 12pm – 1pm
DSpace@MIT archives and makes globally discoverable the research output of MIT faculty, researchers, and students. The session will highlight MIT Libraries’ initiatives for easy upload of complete technical report and working papers series’ and will demonstrate how individuals and research groups can establish and begin populating new collections of research materials.
Contact: Craig Thomas

BLAST
Wednesday, July 29, 11am – 12pm
Learn how to use NCBI resources and optimize your BLAST protein searches to get the most out of your results. Attendance at Bioinformatics for Beginners and familiarity with BLAST are recommended.
Contact: Amy Stout

Data Management 101
Friday, July 31, 12pm – 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 and other relevant issues.
Contact: Anne Graham

Sponsored by the MIT Libraries.

from Thursday May 14th at 8am to Friday, May 22nd at 7pm.

Overnight hours are for the MIT community only.

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

**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!

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!

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.

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.

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.

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.

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.

CITATION MANAGEMENT

• EndNote Basics
• RefWorks Basics
• Managing Your References: Overview of EndNote, RefWorks and Zotero

DATA, DOCUMENT AND IMAGE MANAGEMENT

• Finding Research Datasets: ICPSR and the Harvard-MIT Data Center
• Make your Paper File Cabinets Searchable: How to Manage Paper and Electronic Documents Effectively
• Managing Research Data 101
• QUOSA Information Manager Demo: Retrieve and Organize Article PDFs

BIOINFORMATICS

• BIOBASE Knowledge Library and Explain Analysis System Training
• Bioinformatics for Beginners
• Practically Genomic
• Using NCBI’s BLAST

GIS

• Introduction to GIS Using ESRI ArcGIS Desktop
• Introduction to GIS Using Free Software Tools and Data
• Introduction to Google Maps API
• Mapping and Using US Census Data
• Model Builder
• Open Source and Free Mapping Tools
• Site Selection – Making Spatial Decisions Using a GIS
• Using Elevation Data and Hydrographic Tools in a 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.

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.

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.

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.

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.

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.

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.

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.

More Bioinformatics Resources.

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…

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

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.

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.

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.

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.

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.

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.