Bioscreencast Library

Here is a video demonstration of the DimReduction GUI use.

2008-06-24T15:03:02.00Z

This project involves the development of an interactive software written in Java language for dimensionality reduction, pattern recognition, design and comparative analysis of classifiers.
Author tags:feature selection ,dimensionality reduction ,gene network identification and pattern recognition.

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

2008-06-12T15:03:02.00Z

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 completion
Author tags:pymol ,pymol-idle ,python

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

2008-05-25T23:10:51.00Z

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.
Author tags:Geneious ,bioinformatics tool ,software

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

2008-05-25T23:14:17.00Z

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

2008-05-25T23:23:54.00Z

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

2008-05-25T23:24:18.00Z

intro to Nature Network

2008-05-12T11:54:25.00Z

intro to Nature Network
Author tags:science ,social networkgin

intro to Nature Network, NPG social networking site for scientists

2008-04-30T10:28:10.00Z

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.
Author 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

2008-04-02T15:03:07.00Z

How to use NCBI MapViewer to "pull" DNA sequence from the 5' end of a gene to use in a promoter search
Author tags:promoter ,transcription factors ,NCBI

Web Based Resources for Today's Researcher

2008-02-28T15:03:06.00Z

Web Based Resources for Today's Researcher
Author tags:cu ,iphy ,pascoe ,paperless ,phd ,pdf ,profskills ,papers ,nnw ,rss ,pubmed

Description of a Measurement Kit for BioBrick Promoters and RBSs.

2008-02-27T14:30:16.00Z

Presented at BFF workshop.
Author tags:synthetic biology

Signing up for Pownce

2008-02-26T20:16:53.00Z

A visual add on signing up for Pownce
Author tags:Apps

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

2008-02-24T15:03:07.00Z

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

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

2008-02-24T15:03:06.00Z

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

How I use delicious for my research needs.

2008-02-24T15:03:05.00Z

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

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

2008-02-24T15:03:08.00Z

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

Using Thomson ISI WoK to obtain Journal Impact Factors.

2008-02-24T15:03:04.00Z

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

How to search the ProQuest dissertations online.

2008-02-24T15:03:03.00Z

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

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

2008-02-24T15:03:07.00Z

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

Google Calendar

2008-02-22T19:24:32.00Z

Google Calendar
Author tags:google calendar

short intro to Nature Network the social networking site for scientists

2008-02-15T17:33:51.00Z

How to use Equation Editor

2008-02-01T15:03:00.00Z

How to use Equation Editor
Author tags:word equation

A screencast about BioMedExperts

2008-01-31T15:03:02.00Z

A quick screencast about BioMedExperts
Author tags:Social Networking ,Science

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

2007-12-10T15:03:03.00Z

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.
Author tags:Nature Protocols ,help ,subscription ,access

SigmaPlot - Tips

2007-12-07T23:37:31.00Z

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 Doesn't 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 SigmaPlot's Automation Automate complex repetitive tasks Tap into SigmaPlot's powerful capabilities from other applications
Author tags:SigmaPlot ,graphing ,analysis ,regression ,curvefitting

A demonstration of the CARMEN data porta

2007-11-11T13:42:54.00Z

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

An introduction to Papers by Mike Pascoe

2007-11-09T10:26:02.00Z

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.
Author tags:Papers ,PDF ,tutorial ,organizing ,library ,articles

Resizing of images in Paint

2007-11-07T15:03:02.00Z

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.php
Author tags:paint resize "Protocols Network" "Nature Network" image

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

2007-11-07T12:12:48.00Z

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.php
Author tags:Nature Protocols Network Protocols table 448 pixes

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

2007-11-07T23:13:31.00Z

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

How I create PDFs of scientific articles.

2007-11-07T23:41:11.00Z

How I create PDFs of scientific articles.
Author tags:papers

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

2007-11-06T19:43:33.00Z

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.
Author tags:illiad papers pascoe pubmed pdf article organization research

2.1 - Getting Data

2007-10-17T15:03:06.00Z

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

2.2 - Getting ENCODE data

2007-10-17T15:03:08.00Z

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

2.3 - Text Manipulations

2007-10-17T15:03:04.00Z

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

2.4 - Filtering, Sorting, Joining and Comparing

2007-10-17T15:03:06.00Z

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

2.5 - Fetch Multiple Alignments for Genomic Locations

2007-10-17T15:03:00.00Z

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

2.6 - Filter Multiple Alignments and Convert Formats

2007-10-17T15:03:07.00Z

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

2.7 - Getting Genomic Scores

2007-10-17T15:03:06.00Z

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

3.1 - Preparing data

2007-10-17T15:03:06.00Z

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

3.2 - Intersect and Subtract

2007-10-17T15:03:09.00Z

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

3.3 - Merge and Concatenate

2007-10-17T15:03:09.00Z

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

3.4 - Base coverage and Complement

2007-10-17T15:03:09.00Z

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

3.5 - Coverage

2007-10-17T15:03:04.00Z

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

3.6 - Cluster

2007-10-17T15:03:09.00Z

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

3.7 - Join

2007-10-17T15:03:01.00Z

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

4.1 - Finding NonGencode ESTs Part A

2007-10-17T15:03:01.00Z

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

4.2 - Finding NonGencode ESTs Part B

2007-10-17T15:03:09.00Z

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

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

2007-10-17T15:03:03.00Z

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

4.4 - Finding Non-Gencode ESTs under purifying selection

2007-10-17T15:03:06.00Z

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

5.1 - How to install Galaxy on your machine

2007-10-17T15:03:08.00Z

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