The Bioscreencast Library - Category :: All

The use of templates in the Chemtools LaBLog.

Sun, 03 Aug 08 00:00:00 +0100

Screencast describing the use of templates in the Chemtools LaBLog. Templates are useful both from the perspective of making it easy to record commonly carried out procedures but also are an effective way of maintaining consistency in the metadata.CREATOR TAGS:LaBLog, chemtools, blog, ELN, laboratory notebook,

DimReduction-Feature Selection

Wed, 16 Jul 08 00:00:00 +0100

Video demonstration of the DimReduction GUI use to the feature selection and classification approach. Visit DimReduction project at http://dimreduction.incubadora.fapesp.brCREATOR TAGS:Dimensionality Reduction; Bioinformatics; Pattern Recognition; Feature Selection; Graphic Visualization; Genetic Network; Classification; Java;

DimReduction-Genetic Networks

Wed, 16 Jul 08 00:00:00 +0100

Learn an API like the pymol API with code-completion and syntax highlighting from within IDLE

Thu, 12 Jun 08 00:00:00 +0100

IDLE is great python IDE ( integrated development environment) and is available free with every python installation. Here we demonstrate how IDLE will allow for learning an API in a quick and easy way thanks to syntax highlighting , syntax prompts and code completionCREATOR TAGS:pymol, pymol-idle, python

Overview of Geneious Pro and a brief introduction to the interface layout.

Sun, 25 May 08 00:00:00 +0100

Geneious combines all the major DNA and protein sequence analysis tools into one revolutionary software solution! Its ease of use makes bioinformatics accessible to any biologist.CREATOR TAGS:Geneious, bioinformatics tool, software

Data sources in Geneious Pro, using agents to keep your data up to date and collaborating.

Sun, 25 May 08 00:00:00 +0100

Overview of Geneious Pro for sequence assembly, restriction analysis and primer design.

Sun, 25 May 08 00:00:00 +0100

Overview of Geneious Pro for sequence alignment, phylogenetics and teaching bioinformatics.

Sun, 25 May 08 00:00:00 +0100

intro to Nature Network

Mon, 12 May 08 00:00:00 +0100

intro to Nature NetworkCREATOR TAGS:science, social networkgin

intro to Nature Network, NPG social networking site for scientists

Wed, 30 Apr 08 00:00:00 +0100

Nature Network is the online meeting place for you and fellow scientists to gather, talk and find out about the latest scientific news and events. To get an overview of Nature Network, watch this short video.CREATOR TAGS:science, social networking, web 2.0, biology, chemistry, careers, nature network

How to use NCBI MapViewer to pull DNA sequence from the 5 end of a gene to use in a promoter search

Wed, 02 Apr 08 00:00:00 +0100

How to use NCBI MapViewer to pull DNA sequence from the 5 end of a gene to use in a promoter searchCREATOR TAGS:promoter, transcription factors, NCBI

Web Based Resources for Todays Researcher

Thu, 28 Feb 08 00:00:00 +0000

Web Based Resources for Todays ResearcherCREATOR TAGS:cu, iphy, pascoe, paperless, phd, pdf, profskills, papers, nnw, rss, pubmed

Description of a Measurement Kit for BioBrick Promoters and RBSs.

Wed, 27 Feb 08 00:00:00 +0000

Presented at BFF workshop.CREATOR TAGS:synthetic biology

Signing up for Pownce

Tue, 26 Feb 08 00:00:00 +0000

A visual add on signing up for PownceCREATOR TAGS:Apps

A demo of how to request a digital scan of a paper using ArticleReach Direct

Sun, 24 Feb 08 00:00:00 +0000

See the scribd.com slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

An overview of the uses of the VPN clients and interfaces.

Sun, 24 Feb 08 00:00:00 +0000

See the suggested scribd slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

How I use delicious for my research needs.

Sun, 24 Feb 08 00:00:00 +0000

See the scribd slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

How I use Google Docs to collaborate with other research helpers.

Sun, 24 Feb 08 00:00:00 +0000

See the scribd notes for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

Using Thomson ISI WoK to obtain Journal Impact Factors.

Sun, 24 Feb 08 00:00:00 +0000

See the scribd slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

How to search the ProQuest dissertations online.

Sun, 24 Feb 08 00:00:00 +0000

See the scribd slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

A single example of how I got a PDF using WoK but not through PubMed.

Sun, 24 Feb 08 00:00:00 +0000

See the scribd slides for a greater context.CREATOR TAGS:profskills,cu,pascoe,iphy,paperlessphd,pdf,pubmed

Google Calendar

Fri, 22 Feb 08 00:00:00 +0000

Google CalendarCREATOR TAGS:google calendar

short intro to Nature Network the social networking site for scientists

Fri, 15 Feb 08 00:00:00 +0000

How to use Equation Editor

Fri, 01 Feb 08 00:00:00 +0000

How to use Equation EditorCREATOR TAGS:word equation

A screencast about BioMedExperts

Thu, 31 Jan 08 00:00:00 +0000

A quick screencast about BioMedExpertsCREATOR TAGS:Social Networking, Science

A guide for Nature Protocols authors describing how to use their online access code

Mon, 10 Dec 07 00:00:00 +0000

Nature Protocols authors are supplied with a code enabling them to access the site for free for a year. This guide shows them how to set the code up for a subscription.CREATOR TAGS:Nature Protocols, help, subscription, access

SigmaPlot - Tips

Fri, 07 Dec 07 00:00:00 +0000

What can SigmaPlot do for you? SigmaPlot software helps you quickly create exact graphs Graphing software that makes data visualization easy More than 80 2-D and 3-D technical graph types Customize every detail of your charts and graphs Quickly Plot your Data from Existing Graph Templates in the Graph Style Gallery Publish your charts and graphs anywhere Share high-quality graphs and data on the Web Graphing software that also delivers the data analysis tools you need to draw solid conclusions Data Analysis Doesnt Get Any Easier Get more statistical capabilities when you combine SigmaStat with SigmaPlot Use SigmaPlot within Microsoft Excel Use the Regression Wizard to fit data easily and accurately Plot ANY mathematical function Manage your data efficiently Maximize your Productivity with SigmaPlots Automation Automate complex repetitive tasks Tap into SigmaPlots powerful capabilities from other applications CREATOR TAGS:SigmaPlot, graphing, analysis, regression, curvefitting

A demonstration of the CARMEN data porta

Sun, 11 Nov 07 00:00:00 +0000

A demonstration of the current functionality of the CARMEN data portal given at the Society for Neuroscience meeting 2007CREATOR TAGS:carmen portal neuroinformatics

An introduction to Papers by Mike Pascoe

Fri, 09 Nov 07 00:00:00 +0000

Mike Pascoe has created a great introductory screencast for the program Papers, which helps scientists on the Mac to create their personal library of Science.CREATOR TAGS:Papers, PDF, tutorial, organizing, library, articles

Resizing of images in Paint

Wed, 07 Nov 07 00:00:00 +0000

Many websites have restrictions regarding the maximum width of images. It is therefore sometimes necessary to resize an image before uploading on the internet. On the Nature Network or the Protocols Network, for example, the allowed width for images is 448 pixels. This screencast shows how to resize an image using Paint, a program available on most PCs. The image used in the screencast is part of a Network Protocol: Investigating patchiness of spatially organized ecosystems using field and simulated data http://www.natureprotocols.com/2007/09/17/investigating_patchiness_of_sp.phpCREATOR TAGS:paint resize "Protocols Network" "Nature Network" image

Preparing tables that are less than or equal to 448 pixels wide.

Wed, 07 Nov 07 00:00:00 +0000

For many websites, e.g. the Nature Network or Network Protocols, there is a maximum width that uploaded images can be. This screencast shows how to prepare tables that are well resolved and meet the width requirements of such sites. The Network Protocol used in the example is: Production of neuron-preferential lentiviral vectors http://http://www.natureprotocols.com/2007/02/14/production_of_neuronpreferenti.phpCREATOR TAGS:Nature Protocols Network Protocols table 448 pixes

How I read my PubMed rss feeds and import relevant articles into my PDF library.

Wed, 07 Nov 07 00:00:00 +0000

How I read my PubMed rss feeds and import relevant articles into my PDF library.CREATOR TAGS:papers, pdf, article, organization, nnw, rss, feed, mac, osx

How I create PDFs of scientific articles.

Wed, 07 Nov 07 00:00:00 +0000

How I create PDFs of scientific articles.CREATOR TAGS:papers

A video demonstrating how I import my ILLiad requests into my article managing application Papers.

Tue, 06 Nov 07 00:00:00 +0000

When I cannot find an article through the publisher I submit a request through the ILLiad service. In most cases a scanned PDF is emailed to my inbox and I can then add this to my library.CREATOR TAGS:illiad papers pascoe pubmed pdf article organization research

2.1 - Getting Data

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.1 - Getting Data (4 min 38 sec | 37 MB)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.2 - Getting ENCODE data

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.2 - Getting ENCODE data (2 min 01 sec | 16 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.3 - Text Manipulations

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.3 - Text Manipulations (3 min 48 sec | 19 MB)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.4 - Filtering, Sorting, Joining and Comparing

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.4 - Filtering, Sorting, Joining and Comparing (7 min 22 sec | 63 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.5 - Fetch Multiple Alignments for Genomic Locations

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.5 - Fetch Multiple Alignments for Genomic Locations (6 min 28 sec | 48 MB)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.6 - Filter Multiple Alignments and Convert Formats

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.6 - Filter Multiple Alignments and Convert Formats (7 min 06 sec | 25 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

2.7 - Getting Genomic Scores

Wed, 17 Oct 07 00:00:00 +0100

Screencast 2.7 - Getting Genomic Scores (3 min 26 sec | 26 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.1 - Preparing data

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.1 - Preparing data (2 min 01 sec | 8 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.2 - Intersect and Subtract

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.2 - Intersect and Subtract (7 min 40 sec | 28 MB)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.3 - Merge and Concatenate

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.3 - Merge and Concatenate (6 min 23 sec | 41 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.4 - Base coverage and Complement

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.4 - Base coverage and Complement (2 min 05 sec | 4 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.5 - Coverage

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.5 - Coverage (2 min 14 sec | 14 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.6 - Cluster

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.6 - Cluster (6 min 44 sec | 30 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

3.7 - Join

Wed, 17 Oct 07 00:00:00 +0100

Screencast 3.7 - Join (3 min 36 sec | 36 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

4.1 - Finding NonGencode ESTs Part A

Wed, 17 Oct 07 00:00:00 +0100

Screencast 4.1 - Finding NonGencode ESTs Part A (6 min 51 sec | 54 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

4.2 - Finding NonGencode ESTs Part B

Wed, 17 Oct 07 00:00:00 +0100

Screencast 4.2 - Finding NonGencode ESTs Part B (3 min 48 sec | 32 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

4.3 - Looking for protein-coding transcripts among Non-Gencode ESTs

Wed, 17 Oct 07 00:00:00 +0100

Screencast 4.3 - Looking for protein-coding transcripts among Non-Gencode ESTs (4 min 48 sec | 56 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

4.4 - Finding Non-Gencode ESTs under purifying selection

Wed, 17 Oct 07 00:00:00 +0100

Screencast 4.4 - Finding Non-Gencode ESTs under purifying selection (3 min 28 sec | 29 MB)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

5.1 - How to install Galaxy on your machine

Wed, 17 Oct 07 00:00:00 +0100

Screencast 5.1 - How to install Galaxy on your machine (3 min 23 sec | 28 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

5.2 - How to add tool to Galaxy

Wed, 17 Oct 07 00:00:00 +0100

Screencast 5.2 - How to add tool to Galaxy (8 min 52 sec | 29 MB) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

6.1 - Getting data from UCSC Table Browser and displaying data in UCSC Genome Browser

Wed, 17 Oct 07 00:00:00 +0100

Screencast 6.1 - Getting data from UCSC Table Browser and displaying data in UCSC Genome BrowserCREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

6.2 - How you can use Galaxy to display custom track at UCSC Genome Browser

Wed, 17 Oct 07 00:00:00 +0100

Screencast 6.2 - How you can use Galaxy to display custom track at UCSC Genome Browser CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

7.1 - Prototype: Visualizing alignments with Galaxy and GMAJ

Wed, 17 Oct 07 00:00:00 +0100

Screencast 7.1 - Prototype: Visualizing alignments with Galaxy and GMAJ CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

Supporting Protocol 3 - Extracting alignments in Galaxy

Wed, 17 Oct 07 00:00:00 +0100

Supporting Protocol 3 - Extracting alignments in Galaxy (5 min 12 sec)CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

Supporting Protocol 4 - Bacterial data in Galaxy

Wed, 17 Oct 07 00:00:00 +0100

Supporting Protocol 4 - Bacterial data in Galaxy (11 min 13 sec) CREATOR TAGS:galaxy,bioinformatics,psu,Pennstate,interactive,reproducible,genomics

Four protein files are given in PDB-format on the Desktop. Loading, alignment and superpostition.

Fri, 28 Sep 07 00:00:00 +0100

This movie explains how proteins are displayed three-dimensionally.Four protein files are given in PDB-format on the Desktop. They areloaded by Drag-And-Drop and aligned. The 3D-backbone view is openedfor one protein. The others are dragged into this view to show allproteins in the same view. They are superimposedthree-dimensionally. A PyMOL view is opened and the interoperabilitydemonstrated.CREATOR TAGS:superimpose (superpose) proteins given as pdb files using strap

Bradley Malaria Research Overview

Thu, 27 Sep 07 00:00:00 +0100

This is a talk given on September 26, 2007 to incoming graduate students at Drexel Universlity to brief them on research done in the Bradley lab. The CombiUgi project and how it is being used to synthesize anti-malaria and anti-tumor agents is described along with the basics of Open Notebook Science.CREATOR TAGS:usefulchem, malaria, open science, open notebook science, drexel

Communication platform for scientists

Sat, 22 Sep 07 00:00:00 +0100

Your can set your fields of interests, write your own blog, discuss in forums, manage your bibliography and share it as publication listCREATOR TAGS:Blog, forum, bibliography

Tutorial that shows how to use the RCSB PDB website at www.pdb.org.

Mon, 17 Sep 07 00:00:00 +0100

Tutorial that shows how to use the RCSB PDB website. The most up-to-date version of this tutorial will always be available at www.pdb.org.CREATOR TAGS:pdb, structural biology, bioinformatics

An early prototype of the CARMEN data portal

Wed, 12 Sep 07 00:00:00 +0100

A demonstration given at the All Hands meeting in Nottingham, UK 2007 of an early prototype of the CARMEN data portalCREATOR TAGS:CARMEN e-science neuroscience neuroinformatics

A web app to manage your protein or gene list data and to initiate exploratory functional analyses.

Wed, 12 Sep 07 00:00:00 +0100

# The Protein Function Workbench allows users to upload datasets of protein or gene lists, save them, and initiate analyses on them. This tool is part of the Gaggle project at ISB ( http://gaggle.systemsbiology.org/ ) and therefore interacts with components of the Gaggle Systems Biology suite of tools. Communication with these tools is accomplished via the Firegoose firefox pluggin (available from the Gaggle site). Email hramos@systemsbiology.org for more info. recorded 9/6/07. 120 MB. ~8 min.CREATOR TAGS:Gaggle Proteomics Workbench Annotation

Taxonomic distribution of toxins in UniProtKB: this tutorial shows how to search UniProtKB using controlled vocabularies, how to map results to other databases and save results in various formats (text, tab-delimited, XML, RDF/XML), how to export results

Fri, 17 Aug 07 00:00:00 +0100

beta.uniprot.org hands-on: how to search using controlled vocabularies, do database mapping and export results in various formats (Excel, RDF/XML, etc..).CREATOR TAGS:uniprot, protein, sequence database

How to model physical objects in the web ontology language (OWL)

Wed, 15 Aug 07 00:00:00 +0100

How to model physical objects such as organisms equipments and moleculesCREATOR TAGS:ontology, objects, equipment, owl, molecules, chemicals, organism

Extracting multiple alignments with Galaxy

Fri, 03 Aug 07 00:00:00 +0100

This screencast shows how to use Galaxy to extract and stitch multiple alignments corresponding to a series of genomic coordinates. For example, if you have coordinates of protein-coding exons within the human genome you might want to be able to extract alignments of these exons between human, mouse, dog etc. This screencast shows you how.CREATOR TAGS:galaxy, multiple alignments, genomic coordinates, whole-genome alignments

Filterting multiple alignments with Galaxy

Fri, 03 Aug 07 00:00:00 +0100

This screencast shows how to restrict multiple alignments to a subset of species, filter them by length, and convert into FASTA format.CREATOR TAGS:galaxy, multiple alignments, genome-wide alignments

This is a quick introduction to Galaxy

Tue, 31 Jul 07 00:00:00 +0100

Why use Galaxy? It is not a database or a browser. It is an analysis medium that enables multiple tools to be applied to existing data in a simple unified way. Watch this screencast to see for yourself.CREATOR TAGS:Galaxy Usage Example

this screencast shows you how easy it is to record a screencast using camstudio on Windows-XP

Mon, 23 Jul 07 00:00:00 +0100

With Camstudio Screencasts can be made very easily in the avi format from within windows XPCREATOR TAGS:screencast-tutorial,windows-screencast,camstudio

Use the RSS feed feature to get notifications on new screencasts in your area of interest.

Mon, 23 Jul 07 00:00:00 +0100

Get RSS feeds based on category and/or author.Use personalized Google homepage to get RSS feeds.CREATOR TAGS:rss, bioscreencast tutorial, Google personalized homepage, rss reader

How to use the upload feature on bioscreencast.com.

Mon, 23 Jul 07 00:00:00 +0100

Please upload your screencasts to bioscreencast.com. This screencast shows you how. The screencast also talks about adding tags and related URLS for others to learn more about your screencast . Once an upload is done and reviewed for appropriateness by our team it gets released to the bioscreencast library.CREATOR TAGS:bioscreencast tutorial , upload video ,

This video was made as a test during the how to make a screencast using camstudio demo. Has no real content

Mon, 23 Jul 07 00:00:00 +0100

This video was made as a test during the how to make a screencast using camstudio demo. Has no real content. USed for proof of principle demo puposes for bioscreencastwikiCREATOR TAGS:demo camstudio video , screencast tutorial

This is a screencast of how to use JSpecView (created by Robert Lancashire) to analyze NMR spectra from an experiment involving the synthesis of anti-malarial compounds. It demonstrates the utility of delving deeply into the raw data of failed experiment

Sat, 30 Jun 07 00:00:00 +0100

CREATOR TAGS:JSpecView, NMR, organic, chemistry, imine, JCAMP, spectroscopy

Greasemonkey script that runs inside firefox browser and adds an Add to connotea icon next to each reference in pubmed

Thu, 28 Jun 07 00:00:00 +0100

If you want to add a citation direct from pubmed to connotea , this greasemonkey script adds a small Add to Connotea icon next to each reference and makes it possible to click and add your references into your connotea library from within pubmed CREATOR TAGS:PUBMED,Connotea,Greasemonkey ,Pierre Lindenbaum, Pubmed2Connotea,Javascript, Citation, NCBI,firefoxaddin,Greasemonkey script

Assembling and checking sequencing reaction reads in Seqman to generate consensus sequence after end trimming vector sequences

Thu, 28 Jun 07 00:00:00 +0100

Seqman contig assembly. A double ended ABI sequecning run is assembled in Seqman. Prior to assembly the vector sequences that surround the insert are inserted into the Vector Catalog and the Ends trimmed. This tutorial uses the pet46 vector from Novagen as an example. The ABI trace data is assembled , conflicts resolved and consensus sequence exported as seqman projectCREATOR TAGS:contig assembly,seqman,phrap assembly,vector catalog,pet46,consensus sequence ,sequence assembly , Seqman, Lasergene,DNAStar

NCBI filter and setting up oustide links using linkout

Thu, 28 Jun 07 00:00:00 +0100

This tutorial goes through the filters feature available with PUBMED and views pubmed search result filtered by \Only Reviews\ , \Journals published in the last year\. PUBMED allows you to link your libraries full text article service to your MyNCBI account. This way you can directly login to your MyNCBI account and avail of the full text offerings of your institution. CREATOR TAGS:Linkout,NCBI,PUBMED,library connect,Outside tool, Inside Tool,fulltext,pdf

Post Contig assembly In seqman , the sequence is imported into the vector sequence in Seqbuilder and then a plasmid map is made

Thu, 28 Jun 07 00:00:00 +0100

After cDNA contig assembly in Seqman, this tutorial inserts the cDNA into the appropriate vector at the cloned site and then creates a graphical vector map using SeqbuilderCREATOR TAGS:Seqman,Seqbuilder,Vector,Maps,Vector Maps,contig assembly, Lasergene, DNAstar

Backpackit for your data organization and TODOS

Thu, 28 Jun 07 00:00:00 +0100

Use an online wiki or live webpage to save your lab data . Or use it as an electronic lab notebookCREATOR TAGS:Backpackit ,ELN, Backpackit, Custom WIKI,Online notebook,notebook,TODO list

Banana Tool to slip and slide alignments in seqman

Thu, 28 Jun 07 00:00:00 +0100

The banana tool inside seqman is an important tool used to edit assembled ABI trace sequence data when the reads are of a poor quality and the auto assembly does not give very accurate resultsCREATOR TAGS:banana tool,Seqman,Sequence assembly,ABI trace,consensus sequence, reads

Restrict BLAST to specific genome in the database of completed genomes

Thu, 28 Jun 07 00:00:00 +0100

To discover homologs from a specific genome you can restrict your BLAST run to the custom BLAST frontend provided with each genome project page on NCBI. This genome restricted BLAST is also useful for seraching for homologs in un-annotated and incomplete genome sequencing projectsCREATOR TAGS:BLAST,genome specific BLAST,microbial genome BLAST, microbial homolog,bacterial homolog,NCBI

Using precompiled blast - the BLAST link blink

Thu, 28 Jun 07 00:00:00 +0100

This linkout from NCBI has a complete list of BLAST run for all sequence data. Each BLAST run has full graphical summary and pairwise alignment.CREATOR TAGS:BLAST, precompiled,BLAST link,blink, protein BLAST,NCBI,ncbi BLAST

Visualize conserved domains of protein and examine homologous sequences in Jalview a Free alignment viewer

Thu, 28 Jun 07 00:00:00 +0100

Visualize conserved domains of protein and examine homologous sequences in Jalview a Free alignment viewerCREATOR TAGS:Alignment viewer,Colored Alignment,Viewer, MSA editor, CLUSTALW, PFAM ,Jalview,Java

Create Connotea communities to share links and editable content on topics of interest

Thu, 28 Jun 07 00:00:00 +0100

Create Connotea communities to share links and editable content on topics of interest. Connotea communities are wiki pages. Several tags have associated wiki pages on ConnoteaCREATOR TAGS:Reference manager ,Connotea,Communities, wiki

Connotea groups helps multiple connotea users share libraries.

Thu, 28 Jun 07 00:00:00 +0100

Connotea groups helps multiple connotea users share libraries. Groups can have profiles and be private or publicCREATOR TAGS:Reference manager ,Connotea,Groups,Share citations,Citation manager

Finding homologous proteins with architechture that resembles your protein from the database of conserved domains

Thu, 28 Jun 07 00:00:00 +0100

This tutorial describes the use of the conserved domain database. Obtain a graphical summary of conserve domains in your protein of interest. View sequence alignment of conserved domains and your query protein. Search for other proteins with similar architecthures across the microbial world and other eukaryotesCREATOR TAGS:Homologous proteins, Domain architecture,domains in protein, PFAM, CDART, NCBI,Ring domain

Get a list of conserved domains in your protein and also view a sequence alignment and graphic of domain architechture of your protein

Thu, 28 Jun 07 00:00:00 +0100

This tutorial describes the use of the conserved domain database at NCBI. Obtain a graphical summary of conserved domains in your protein of interest. View sequence alignment of conserved domains with your query protein. CREATOR TAGS:CDD, Conserved domains, Protein domain,CDART , PFAM,NCBI

Import sequences that are not in standard forms or as freetext into lasergene applications using Editseq application

Thu, 28 Jun 07 00:00:00 +0100

EditSeq makes it possible to simply copy and paste your sequence for further use in other lasergene applications. Select the sequence from web browser and simply drop in rhe sequence, Editseq edits out the non Protein or DNA sequence charactersCREATOR TAGS:Lasergene , Seqedit , Sequence Import, import, DNASTAR

Use unique pubmed ID , PMID to import citations into pubmed library

Thu, 28 Jun 07 00:00:00 +0100

This demo first connects to NCBI Pubmed using a connection file . Then we Use unique pubmed ID , PMID to import citations into an EndNote libraryCREATOR TAGS:Endnote,PMID,Citation import, PUBMED,reference manager

Identify unique cutting sites in Nucleic acid DNA sequence using Seqbuilder

Thu, 28 Jun 07 00:00:00 +0100

Unique sites in DNA sequence mapped onto sequence using SeqBuilderCREATOR TAGS:Unique sites,Restriction map, Seqbuilder , Enzyme, cutting sites,

Straight line plot of data with linear regression followed by plot of fitted line with error bars

Thu, 28 Jun 07 00:00:00 +0100

Import of data into Excel followed by setting up the statistical analysis package in excel. Fitting data to a Straight line with linear regression followed by plot of fitted line and displaying standard deviation with error bars. CREATOR TAGS:error bars , regression , linear regression ,plotting ,excel chart, standard deviation, straight line

Straight line plot of data with linear regression followed by plot of fitted line with error bars

Thu, 28 Jun 07 00:00:00 +0100

Import of data into Excel followed by setting up the statistical analysis package in excel. Fittinf data to a Straight line with linear regression followed by plot of fitted line anddisplaying standard deviation with error bars. CREATOR TAGS:error bars , regression , linear regression , plot, standard deviation , straight line plot

Look for genomic context of a particular ORF in a microbial genome

Thu, 28 Jun 07 00:00:00 +0100

What genes are around my gene in the microbial genome?. Several times ORFS are clustered in operons. The Genome browser helps look at region around a particular locus. This is also useful to check possible annotation errors like missed start or non-canonical initiation of transcription.CREATOR TAGS:Genome context, DNA locus , locus , mapviewer, genome browser

Using google calendar to organize simple events eg. Lab meetings that recur

Thu, 28 Jun 07 00:00:00 +0100

Tutorial that describes sign ins and initial setup for google calendar. Basic sharing of Calendar among group using ICAL format lead in.CREATOR TAGS:Google Calendar, Events, Calendar, Ical,sharing, Group Events,Scheduling

Creating google groups for version 1.0

Thu, 28 Jun 07 00:00:00 +0100

Google groups are a free service by google to create online groups. These groups can made private or restricted and public. It helps if members have google accounts but this is not necessary. Groups also have locations for wiki pages and files in the new beta version.CREATOR TAGS:groups, Google Groups,email group

Using personalized Google homepage to show PUBMED search results for topic of interest

Thu, 28 Jun 07 00:00:00 +0100

From PUBMED it is easy to create a live feed results for any search. SO now like a news ticker or a stock ticker you can have live search results that are updated on your personalized google home page daily. This tutorial shows you how.CREATOR TAGS:RSS,PUBMED ,ncbi, live bookmark,google home page

Using google spreadsheets to create basic workbook to import NCBI search result as excel file

Thu, 28 Jun 07 00:00:00 +0100

Google spreadsheets are a nice way to import existing Excel data and share it with collaborators who can then view it online. Google spreadsheets also allow you to collaborate on the document live with several people simultaneously.CREATOR TAGS:Spreadsheet,online spreadsheet, Excel,data sharing, data collaboration, excel collaborate

Inserting custom vector into lasergene suite Vector Catalog

Thu, 28 Jun 07 00:00:00 +0100

The vector catalog provided with the lasergene suite has a few vectors sequences provided with the basic install. This tutorial describes how to add a new vector/plasmid DNA sequence to It and specify the MCS clonig position. This is useful for trimming ends during contig assemblyCREATOR TAGS:Vector catalog , Vector , Plasmid , Import,Seqman, Seqbuilder , pet46

Start Jalview from webpage and overview functionality of Jalview 2.0

Thu, 28 Jun 07 00:00:00 +0100

Jalview is a multiple sequence alignment editor and viewer. This screencast describes basic overview of Jalview user interfaceCREATOR TAGS:MSA align ,alignment viewer, alignment editor, Jalview,colored alignment, MSA,ClustalW , multiple sequence alignment

Create a custom table of contents(TOC) alert for journal of choice using saved serach feature at NCBI.

Thu, 28 Jun 07 00:00:00 +0100

MyNCBI saved searches and email updates are a useful way to setup and manage table of contents alerts for multipl journalsCREATOR TAGS:TOC, NCBI,PUBMED, Email pubmed result,table of contents

Custom filters help you filter or sort PUBMED search results

Thu, 28 Jun 07 00:00:00 +0100

Create custom filters to group results on PUBMED.Group results by review , published in the last five years for eg.CREATOR TAGS:Filters, NCBI, reviews,pubmed, PUBMED

Setting up automatic email of results for query from a selct numbre of journals.

Thu, 28 Jun 07 00:00:00 +0100

Set up a search for results matching keywords for eg.Stem cell niche from Journals Nature, Science and CellCREATOR TAGS:My NCBI ,saved search, email pubmed result, email alert

Save NCBI or PUBMED search results to your own collection.

Thu, 28 Jun 07 00:00:00 +0100

NCBI-PUBMED collections allow you to store references to your personal library. This feature allows you to have different citation libraries for different research projects you undertake.CREATOR TAGS:My NCBI, NCBI collections, saved results, pubmed

You can send your sequence from NCBI to a genbank file and use seqbuilder from within the DNAstar suite to examine and analyze your sequence

Thu, 28 Jun 07 00:00:00 +0100

Export your sequence data from NCBI in the genbank format for use in seqbuilder. After import into Seqbuilder you can customize the layout by hiding translation strands, showing sequence features, view nucleotide sequence as codon triplets and save the customized layout.CREATOR TAGS:Seqbuilder, Sequence export,NCBI, genbank file , Seqbuilder layout , Send to File

Export mutliple sequences into XML format for import into microsoft Excel

Thu, 28 Jun 07 00:00:00 +0100

The TinySeqXML format can be exported from Entrez/NCBI . When you have multiple sequences with annotations from a search result at NCBI you can seamlessly export them to Excel. Excel reads TinySeqXML format and creates a table with sequence information for easy analysis and sorting. These Excel files can also be shared using an online speadhseet like google spreadsheets CREATOR TAGS:XML export, NCBI , TinySeqXML, NCBI to Excel, Excel , sequence export, fasta

Create custom Live bookmark or RSS feed for searh results and keep uptodate using feed reader

Thu, 28 Jun 07 00:00:00 +0100

Do you want your google homepage or yahoo front page to have PUBMED search results for your topics of interest. Create an RSS feed at PUBMED and add this feature to your RSS reader. Now just like news and sports highlights you can get publication highlights with your favorite RSS readerCREATOR TAGS:RSS feed, PUBMED, RSS, literature alert, Google home, NCBI , Google

Setup of connecting PUBMED to some libraries using a password validated login available via the library ( outside tool ).

Thu, 28 Jun 07 00:00:00 +0100

Setup of connecting PUBMED to some libraries using a password validated login available via the library ( outside tool ). CREATOR TAGS:Outside tool, PUBMED, full-text, NCBI linkout, NCBI , brandeis library

Visualize multiple sequence alignments for homogous protein sequences from the Protein families database

Thu, 28 Jun 07 00:00:00 +0100

What does residue 54 in my protein sequence correspond to in another protein homolog. The PFAM and Jalview combination helps visualize and edit multiple sequence alignments.CREATOR TAGS:Protein families,sequence alignment, PFAM, alignment viewer, PFAM to Jalview, Protein homology viewer, sequence homology, MSA, multiple sequence alignment

Getting non redundant ( unique) sequences for protein or ORF is easy with the Refseq database.

Thu, 28 Jun 07 00:00:00 +0100

The Refseq database is present as a standard filter with NCBI search. The database of non redudan sequences is good for understanding true homologs for any protein sequenceCREATOR TAGS:unique sequence,Refseq, Genbank, GI,non redundant sequences,unique sequences

Import sequence into Seqman vector catalog

Thu, 28 Jun 07 00:00:00 +0100

Import sequence into Seqman vector catalogCREATOR TAGS:Vector catalog , Vector , Plasmid , Import plasmid , Seqman , Seqbuilder, Lasergene, DNAStar, end trim, sequence assembly, abi trace assembly

If you need a chemical or want to find a related chemical subsrtucture search is a powerful way to look for it in the sigma catalog

Thu, 28 Jun 07 00:00:00 +0100

If you cannot locate a particualr chemical in the sigma chemical database. Substructure query helps you find chemicals by structure. Sustructure query also helps you find chemicals which are similar to a particular structureCREATOR TAGS:substructure search , related chemical, chemical compound, substructure, SMILES

Using multiple query styles available with NCBI databases to get at information.

Thu, 28 Jun 07 00:00:00 +0100

Query a genome for a sequence file using HISTORY option to setup advanced query. Once a particular subset of sequences is obtained you can easily export the nucelotide sequence for ORF of interest to a genbank format sequence fileCREATOR TAGS:NCBI, search strategy, ORF genome query,export genbank file, sequence export,entrez search

Use backpackit to organize your research projects

Thu, 28 Jun 07 00:00:00 +0100

Backpackit provides features to create custom password protected wiki pages. Create shared documents. Create TODOSCREATOR TAGS:writeboard, Backpackit, collaborative document, wiki , data organization

How do I find out when fresh annotations are added to my newly sequenced organism- Saved searches and email alerts show you how

Thu, 28 Jun 07 00:00:00 +0100

The Entrez query system is very powerful to ask specific questions by querying several Entrez databases. In this example we look for all genes involving chloride transport in Bacteroides thetaiotaomicron. Once we construct the query using the History option. We setup email alerts for the query to monitor any future annotations in the organisms genome.CREATOR TAGS:refining search, NCBI-refining search, My NCBI, MyNCBI, saved search NCBI, Entrez saved search

Query NCBI/Entrez for swissport id and save fasta sequence to file

Thu, 28 Jun 07 00:00:00 +0100

In this tutorial we query the NCBI/Entrez databases for P32923 a protein swissprot id. Once the protein is located we save the fasta protein sequence file to the local disk.CREATOR TAGS:fasta sequence , swissprot id, NCBI, Entrez, send to file

Connotea- create login, add citation and discover new content using added citations

Thu, 28 Jun 07 00:00:00 +0100

In this tutorial we create a new connotea login. We then setup our internet browser to post links and citations to connotea. After browser setup, we explore connotea as a tool to add and importantly, discover new content.CREATOR TAGS:connotea, social bookmarking, new content,introduction

Create and refine queries in PUBMED and NCBI databases using Preview and Index

Thu, 28 Jun 07 00:00:00 +0100

In this tutorial we look for all reviews on a particular topic Rotavirus authored by a particular author. This screencast uses the Preview and Index options within NCBI to intelligently create and refine queries.CREATOR TAGS:refine query, PUBMED, preview and index, search strategy,entrez, NCBI

Saved searches help one keep track of new publications matching a search criterion

Thu, 28 Jun 07 00:00:00 +0100

In this tutorial we login to MyNCBI and monitor what new citations match a saved searchCREATOR TAGS:saved search, new citations,PUBMED, ncbi

Designing Primers with Primer Select from DNASTAR

Thu, 28 Jun 07 00:00:00 +0100

This tutorial takes you through the Primer Select Program from DNASTAR to design primers. CREATOR TAGS:primer design, primer select, cloning, pcr

This screencast shows you how to download and use the mac desktop widget to search the bioscreencast library

Thu, 28 Jun 07 00:00:00 +0100

The bioscreencast mac dashboard widget is light weight, and you can use it to browse topics of interest and view screencasts on the bioscreencast library right from your desktopCREATOR TAGS:screencast, tutorial, dashboard, widget

This briefly goes through different features on the website and gives a general overview of bioscreencast.com

Wed, 27 Jun 07 00:00:00 +0100

The features covered under this tutorial are: different tabs on the main page and features specific to users who log in. CREATOR TAGS:main-page, navigate, general-overview, screencast, tutorial

This shows you how to request a screencast on bioscreencast.com

Tue, 26 Jun 07 00:00:00 +0100

How to use all the features on the request screencast page. Voting, filling in the form, editing your requestCREATOR TAGS:request, screencast, tutorial

Features while playing each movie

Tue, 26 Jun 07 00:00:00 +0100

How to use the features on the menu toolbar while playing each screencast - related videos, weblinks, comments, tagging, embed etc.CREATOR TAGS:screencast, tutorial, menu

IshowU from shinywhitebox.com is a great screencasting tool for the mac.

Mon, 25 Jun 07 00:00:00 +0100

This 1 min tutorial tells you how easy it is to get screencasting on the mac with IshowU. For just $20 you can make a screencast. IshowU also allows you to save it to your ipod and export it to se veral other formatsCREATOR TAGS:screencast-tutorial,shinywhitebox,ishowU,mac-screencast

This tutorial describes the installation procedure for camstudio on a windows machine

Mon, 25 Jun 07 00:00:00 +0100

To install camstudio you first install the camstudio codec and then install the main application. This screencast goes through the installation of camstudio on windows XP.CREATOR TAGS:screencast-tutorial,camstudio,windows-screencast

Use Pymol alignment of two protein structure

Mon, 11 Jun 07 00:00:00 +0100

Pymols alignment algorithm aligns two structures and gives us an rmsd between two proteinsCREATOR TAGS:pymol,superpose,align

The MPDB or membrane protein databank is a collection of data and statistics on all aspects of membrane protein expression, solubilization and crystallization

Thu, 12 Apr 07 00:00:00 +0100

Membrane protein databank has a lot of compiled and elegantly displayed statistics on every aspect of membrane proteins structural biology ranging from the the expression systems and source organisms used to the detergents , additives and phasing methodology used for structure solution.CREATOR TAGS:membrane-protein,crystallization,detergent,statistics,structural biology

Precompiled BLAST link at NCBI to look for homologous proteins

Sun, 01 Apr 07 00:00:00 +0100

The precompiled BLAST link- Blink at the NCBI offer a very convenient way to run a BLAST search against any given sequence. This screencast first finds a particular protein in the database and then investigates the Blink BLAST resultsCREATOR TAGS:blink, BLAST, NCBI, homolog, precompiled-blast

Pymol screencast that shows you how to load a pdb file and make a cartoon ribbon diagram image of a protein structure

Sun, 01 Apr 07 00:00:00 +0100

Pymol is a an excellent program for protein structure visualization and analysis. In this screencast we load a pdb file into pymol and using the preset representations in pymol we render a high resolution image of a cartoon representation for a protein structure .CREATOR TAGS:pymol,preset-image,ribbon diagram,publication image,protein structure

Design primers with mutations using DNAStars primer select

Wed, 07 Mar 07 00:00:00 +0000

This is the second tutorial of primer select which explains how to modify the length of the primer and how to introduce a mutation in the primer. This tutorial uses DNAStars primer select tool.CREATOR TAGS:cloning, primer design, mutation, primer modification