Bioinformatics

IAP 2010: Bioinformatics for Beginners

Posted January 5th, 2010 by Ryan Gray

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 6, 11am – 12pm & Tuesday, January 12, 3 – 4pm

WHERE: DIRC, 14N-132

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

Contact Erja Kajosalo with any questions.

Check out the MIT Libraries’ full schedule of IAP sessions.

This session is co-sponsored by the Electrical Engineering and Computer Science department.

Check out the MIT Libraries’ IAP 2010 sessions!

Posted December 11th, 2009 by Ryan Gray

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 kick back and enjoy a film festival, improve your bioinformatics search skills, or learn how to make your own videos for the Web?

Look no further! Take a peek at all of the MIT Libraries IAP Activities offered in 2010.

New Bioinformatics Resource Available! Human Gene Mutations Database (HGMD)

Posted August 11th, 2009 by Ryan Gray

HGMD database logo
MIT Libraries has obtained a license for the Human Gene Mutations Database (HGMD). HGMD represents a comprehensive collection of data available on germ-line mutations in nuclear genes underlying or associated with human inherited disease.

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.

JulyAP 2009 Workshop: Bioinformatics for Beginners

Posted July 6th, 2009 by Ryan Gray

Bioinformatics

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

JulyAP 2009 Workshop: GeneGo Training

Posted July 6th, 2009 by Ryan Gray

GeneGo logo

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

Broad Institute and MIT Libraries

Posted June 29th, 2009 by Ryan Gray


The Broad Institute will transition from a department within MIT to a permanent non-profit organization on July 1, 2009. Broad employees who are affiliated with MIT as faculty or staff will continue to have borrowing privileges and access to the MIT Libraries’ collections, while all other Broad employees will no longer have the same access.

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.

JulyAP 2009 Workshops

Posted June 26th, 2009 by Ryan Gray


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.

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.

Hayden Open 24 hours, May 14-22 for Finals

Posted May 14th, 2009 by mit-admin

Hayden Library — Humanities & Science — will stay open 24 hours a day during Finals

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

Overnight hours are for the MIT community only.

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.