Search Results for: zebrafish behavior

The facilities at AIM are available for use by the entire NIH intramural research community. While we welcome users with any size imaging project, AIM specializes in large, yearlong (or longer), collaborative research efforts with Read More...

01/10/2024 - Our series of talks continues next month with two 20-minute presentations focused on single cell genomics studies in the model organism zebrafish.  There will be light refreshments and we encourage attendees to Read More...

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11/07/2024 - Dr. Blackshaw's work investigates the molecular mechanisms controlling neurogenesis and cell fate specification in the vertebrate forebrain, with a particular focus on the retina. He currently focuses on the use of comparative S Read More...

09/12/2024 - Dr. Nussinov will highlight some scientific questions bordering on physics and biology, where fundamental physics and chemistry can help biology. They span the behavior of a bird, protein activation, signaling in cancer, and neurodevelopmental Read More...

01/03/2024 - on Wednesday, January 3rd at noon in Building 41, Conference Room C507/C509 and online. In-person attendance is encouraged.  Dr. Larson's research is focused on understanding gene expression in eukaryotic Read More...

12/12/2023 - Dr. Anant Madabhushi and his team have been developing computerized knowledge alignment, representation, and fusion tools for integrating and correlating heterogeneous biological data spanning different spatial and temporal scales, modalities, and functionalities. These tools Read More...

10/19/2022 - Speaker: Ron Germain, M.D., Ph.D. NIH Distinguished Investigator NIAID, NIH Dr. Germain received his Sc.B. and Sc.M. from Brown University in 1970 and his M.D. and Ph.D. from Harvard Read More...

06/16/2021 - Register/Join The genetic variation found among individuals results in patterns of polymorphisms passed down through generations. This evolutionary variation typically holds true for individuals, samples from the same population or subpopulation, and cells Read More...

09/30/2020 - Register Through large collaborative research projects, the field of neuroscience is gaining access to unprecedented amounts of information about the structure and function of the brain. These datasets are already having a profound impact Read More...

To view the files and subfolder within a directory, the ls command can be used. For instance, ls will retrieve the following items in a directory when issued. file.txt Recall that Unix commands come Read More...

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

To view the files and subfolder within a directory, the ls command can be used. For instance, ls will retrieve the following items in the unix_demonstration directory when issued. file.txt Recall that a Read More...

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

Colors are assigned to the fill and color aesthetics in aes(). We can change the default colors by providing an additional layer to our figure. To change the color, we use the scale_color functions: Read More...

Now that we have accession numbers to work with, let's use parallel and fastq-dump to download the data. GNU parallel is a shell tool for executing jobs in parallel using one or more computers. Read More...

The formula: VLOOKUP(lookup_value, table_array, col_index_num, [range_lookup]) In its simplest form, the VLOOKUP function says: =VLOOKUP(What you want to look up, where you want to look for it, the Read More...

As with any language, the learning curve for Unix can be quite steep. However, to work on Biowulf you really need to understand the following: Navigating the File System: Understanding the hierarchical structure of directories, Read More...

As with any language, the learning curve for Unix can be quite steep. However, to work on Biowulf you really need to understand the following: Navigating the File System: Understanding the hierarchical structure of directories, Read More...

11/12/2024 - Join us at the upcoming hybrid NIH BRAIN NeuroAI Workshop on November 12 and 13, with virtual access to in-person panels and discussions at the NIH Campus in Bethesda, MD. Artificial intelligence (AI) is reshaping technology Read More...

The "parallel" tool executes commands in "parallel", one for each CPU core in your system. See Tool: Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them cat runids.txt | Read More...

GNU parallel executes commands in "parallel", one for each CPU core on your system. It can serve as a nice replacement of the for loop . See Tool: Gnu Parallel - Parallelize Serial Command Read More...

Now that we have accession numbers to work with, let's use parallel and fastq-dump to download the data. GNU parallel executes commands in "parallel", one for each CPU core on your system. Read More...

At this point, you have seen the term "factor" pop up a few times. Factors can be thought of as vectors which are specialized for categorical data. Given R’s specialization for statistics, Read More...

11/02/2022 - Join Emory University’s Dr. Anant Madabhushi as he discusses the   Center for Computational Imaging and Personalized Diagnostics ’ (CCIPD’s) development work on new radiomic and pathomic approaches for capturing intra-tumoral heterogeneity and modeling Read More...

10/20/2021 - Presenter: Trevor Bedford, Ph.D. Associate Professor Vaccine and Infectious Disease Division Human Biology Division Herbold Computational Biology Program Fred Hutchinson Cancer Research Center Genomic epidemiology has enabled critical insights during the COVID-19 pandemic.  Read More...

01/25/2021 - Presenter: Dr. Arjun Raj from the Perelman School of Medicine, UPenn. Abstract:Anti-cancer therapies can often kill the vast majority of tumor cells but a few rare cells remain and grow despite treatment. Non-genetic Read More...

02/12/2020 - This two-day instructor-led course gives participants a broad study of networking options on Google Cloud Platform. Through presentations, demonstrations, and hands-on labs, learners explore and deploy GCP networking technologies, such as Google Virtual Private Read More...

Go back up one directory to the unix_on_biowulf_2023_documents folder and then change into the SRR1553606 folder. cd .. cd SRR1553606 There are two next generation sequencing data files (fastq files) in this folder. Read More...

Go back up one directory to the unix_on_biowulf_2023_documents folder and then change into the SRR1553606 folder. cd .. cd SRR1553606 There are two next generation sequencing data files (fastq files) in this folder. Read More...

Recall that we are not supposed to use the login nodes to perform any computation intensive tasks on Biowulf. Instead, we should either submit a job (if staying in the log in node) with sufficient Read More...

If this is the first time a personal access token is used, Git will ask to user to supply it. However, Git will store this in the MacOSX keychain or Windows Credential Manager so users Read More...

In Lesson 2, I introduced the idea of command options (flags). Command options allow us to change the behavior of a command. Command options, which ultimately allow you to modify command parameters, are extremely important to Read More...

The Molecular Signatures Database (MSigDB) is a curated resource of thousands of gene sets by the Broad Institute. These sets were curated for use with GSEA software but are used with other tools as well. Read More...

Names should: Avoid spaces or special characters EXCEPT '_' and '.' Not include numbers or symbols at the beginning of an object name. Avoid common names with special meanings (?Reserved) or assigned to existing functions (These will Read More...

Names should: Avoid spaces or special characters EXCEPT '_' and '.' Not include numbers or symbols at the beginning of an object name. Avoid common names with special meanings (?Reserved) or assigned to existing functions (These will Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...

We will build a database out of all features of the 2014 Ebola genome under accession number KM233118. This data will go into a new directory named "db_2014". mkdir -p db_2014 # Get the 2014 Ebola Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Review: * downloading data from SRA * decompressing tar files * e-utilities * fastq-dump Learn: * sra-stat * XML format * automating SRA downloads * working with comma-separated values (csv) format * Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Why Learn Bioinformatics? Analyze your own data Expand scientific training and skills Provide a path to a new career Have a better understanding of how other people analyze data What is Unix? an operating system, Read More...

Lesson 6: sra-tools, e-utilities, and parallel This page uses some content directly from the Biostar Handbook by Istvan Albert. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch or swarm Read More...

Lesson 6: Downloading data from the SRA For this lesson, you will need to login to the GOLD environment on DNAnexus. Lesson 5 Review: The majority of computational tasks on Biowulf should be submitted as jobs: sbatch Read More...

This page uses content directly from the Biostar Handbook by Istvan Albert. Remember to activate the bioinformatics environment and create a directory for today's work. conda activate bioinfo mkdir blast cd blast What is Read More...

Data frames Objectives To be able to load, explore, and access data in a tabular format. To this end, students should understand the following: 1. how to import and export data 2. how to create, summarize, and Read More...

First Unix command (ls) ls You may see something like this: public reads.tar sample.fasta sample.fastq The "ls" command "lists" the contents of the directory you are in. You Read More...