1. National Science Foundation: For the love of science! Head here when searching for ways to pay for that gargantuan geology or bigtime biology project. And other disciplines, of course.
2. Alexander von Humboldt Foundation: Humbolt fellows embody the spirit of science and leadership alike, and the organization sponsors thinkers in Germany and abroad alike.
3. National Parks Foundation: Americans who want to preserve their country’s gorgeous parks and trails pitch projects to this governing body, concerned largely with ecology and accessibility issues.
4. Alfred P. Sloan Foundation: Money is available here throughout the year, covering science and engineering and their overlaps with civics, education, and economics.
5. The Whitehall Foundation: The Whitehall Foundation, through its program of grants and grants-in-aid, assists scholarly research in the life sciences. It is the Foundation’s policy to assist those dynamic areas of basic biological research that are not heavily supported by Federal Agencies or other foundations with specialized missions.
6. Human Frontier Science Program: Research grants from the Human Frontier Science Program are provided for teams of scientists from different countries who wish to combine their expertise in innovative approaches to questions that could not be answered by individual laboratories.
7. The U.S. Small Business Administration: The U.S. Small Business Administration offers research grants to small businesses that are engaged in scientific research and development projects that meet federal R&D objectives and have a high potential for commercialization.
8. The Welch Foundation: The Welch Foundation provides grants for a minimum of $60,000 in funding to support research in chemistry by a full-time tenured or tenure-track faculty member who serves as principal investigator. Applications are restricted to universities, colleges, or other educational institutions located within the state of Texas.
9. The Leakey Foundation: The Leakey Foundation offers research grants of up to $25,000 to doctoral and post-doctoral students as well as senior scientists, for research related specifically to human origins.
10. American College of Sports Medicine: The American College of Sports Medicine offers several possible grants to research students in the areas of general and applied science.
11. BD Biosciences: BD Biosciences Research Grants* aim to reward and enable important research by providing vital funding to scientists pursuing innovative experiments that advance the scientific understanding of disease. This ongoing program includes grants for immunology and stem cell research, totaling $240,000 annually in BD Biosciences research reagents.
12. Sigma Xi: The Sigma Xi program awards grants for research in areas of science, engineering, astronomy and vision.
13. The United Engineering Foundation: The United Engineering Foundation advances the engineering arts and sciences for the welfare of humanity. It supports engineering and education by, among other means, making grants.
14. National Institutes of Health: Foreign and American medical professionals hoping to advance their research might want to consider one of these prestigious (and generous) endowments.
15. Whitaker International Program: Biomedical engineering’s global reach serves as this organization’s focus, so applications here need to open themselves up to international institutions and applications.
16. U.S. National Library of Medicine: From tech to small businesses, the USNLM’s funding programs cover a diverse range of fields that feed into medicine.
17. American Heart Association: Most of the AHA’s research involves cardiovascular disease and stroke, with funding in these areas available in the winter and the summer.
18. Society for Women’s Health Research: Female engineers and scientists benefit from these grants meant to support anything that improves women’s health and education on a global scale.
19. Damon Runyon Cancer Research Foundation: Every cent donated to the DRCRF directly feeds into fellowships and awards bringing humanity closer to cancer cures and improved prevention regimens.
20. Burroughs Wellcome Fund: Emerging scientists working in largely underrecognized and underfunded biomedical fields are the main recipients of this private foundation’s money.
21. The Foundation for Alcohol Research: As one can probably assume from the name, The Foundation for Alcohol Research contributes to projects studying how alcohol impacts human physical and mental health.
22. Alex’s Lemonade Stand: These grants go towards doctors, nurses, and medical researchers concerned with curing childhood cancer.
23. National Cancer Institute: Thanks to a little help from their friends in Congress, the National Cancer Institute have $4.9 billion to share with medical science.
24. Bush Foundation Fellowship Program: Leadership’s many forms are the main focus of the BFFP, who give money to folks dedicated to improving their communities.
25. The David & Lucile Packard Foundation: Nonprofit organizations dedicated to growing education, charities, health, and other social justice causes should consider seeing what money they can land through this foundation.
26. American Federation for Aging Research: AFAR provides up to $100,000 for a one- to two-year award to junior faculty (M.D.s and Ph.D.s) to conduct research that will serve as the basis for longer term research efforts in the areas of Biomedical and clinical research.
27. The Muscular Dystrophy Association: The MDA is pursuing the full spectrum of research approaches that are geared toward combating neuromuscular diseases. MDA also helps spread this scientific knowledge and train the next generation of scientific leaders by funding national and international research conferences and career development grants.
28. The Cystic Fibrosis Foundation: The CF Foundation offers competitive awards for research related to cystic fibrosis. Studies may be carried out at the subcellular, cellular, animal, or patient levels. Two of these funding mechanisms include Pilot and Feasibility Awards and Research Grants.
29. The National Ataxia Foundation: The National Ataxia Foundation (NAF) is committed to funding the best science relevant to hereditary and sporadic types of ataxia in both basic and translational research. NAF invites research applications from U.S.A. and International non-profit and for-profit institutions.
30. The March of Dimes: In keeping with its mission the March of Dimes research portfolio funds many different areas of research on topics related to preventing birth defects, premature birth and infant mortality.
31. The American Tinnitus Association: The American Tinnitus Association Research Grant Program financially supports scientific studies investigating tinnitus. Studies must be directly concerned with tinnitus and contribute to ATA’s goal of finding a cure.
32. American Brain Tumor Association: The American Brain Tumor Association provides multiple grants for scientists doing research in or around the field of brain tumor research.
33. American Cancer Society: The American Cancer Society also offers grants that support the clinical and/or research training of health professionals. These Health Professional Training Grants promote excellence in cancer prevention and control by providing incentive and support for highly qualified individuals in outstanding training programs or responsible for training.
34. Thrasher Research Fund: The Thrasher Research Fund provides grants for pediatric medical research. The Fund seeks to foster an environment of creativity and discovery aimed at finding solutions to children’s health problems. The Fund awards grants for research that offers substantial promise for meaningful advances in prevention and treatment of children’s diseases, particularly research that offers broad-based​ applications.
35. Foundation for Physical Therapy: The Foundation supports research projects in any patient care specialty.
36. International OCD Foundation: The IOCDF awards grants to investigators whose research focuses on the nature, causes and treatment of OCD and related disorders.
37. Susan G. Komen: Susan G. Komen sustains a strong commitment to supporting research that will identify and deliver cures for breast cancer.
38. American Association for Cancer Research: The AACR promotes and supports the highest quality cancer research. The AACR has been designated as an organization with an approved NCI* peer review and funding system.
39. American Thyroid Foundation: The ATA is committed to supporting research into better ways to diagnose and treat thyroid disease.
40. The Foundation for Anesthesia Education and Research: The FAER provides research grant funding for anesthesiologists and anesthesiology trainees to gain additional training in basic science, clinical and translational, health services and education research.
41. The Alzheimer’s Association: The Alzheimer’s Association funds a wide variety of investigations by scientists at every stage of their careers. Each grant is designed to meet the needs of the field and to introduce fresh ideas in Alzheimer’s research.
42. The Arthritis National Research Foundation: The Arthritis National Research Foundation seeks to move arthritis research forward to find new treatments and to cure arthritis.
43. Hereditary Disease Foundation: The focus of the Hereditary Disease Foundation is on Huntington’s disease. Support will be for research projects that will contribute to identifying and understanding the basic defect in Huntington’s disease. Areas of interest include trinucleotide expansions, animal models, gene therapy, neurobiology and development of the basal ganglia, cell survival and death, and intercellular signaling in striatal neurons.
44. The Childrens Leukemia Research Association: The objective of the CLRA is to direct the funds of the Association into the most promising leukemia research projects, and where funding would not duplicate other funding sources.
45. The American Parkinson Disease Association: The APDA offers grants of up to $50,000 for Parkinson disease research to scientists affiliated with U.S. research institutions.
46. The Mary Kay Foundation: The Mary Kay Foundation offers grants to select doctors and medical scientists for research focusing on curing cancers that affect women.
47. The Crohn’s & Colitis Foundation of America: The CCFA is a leading funder of basic and clinical research in Inflammatory Bowel Diseases. CCFA supports research that increases understanding of the etiology, pathogenesis, therapy, and prevention of Crohn’s disease and ulcerative colitis.
48. The Avon Foundation for Women: Grants from the Avon Foundation go to develop new strategies to prevent breast cancer and to researching the science behind breast cancer to increase understanding.
49. The International Research Grants Program: The IRGP seeks to promote research that will have a major impact in developing knowledge of Parkinson’s disease. Effort is made to promote projects that have little hope of securing traditional funding.
50. American Gastroenterological Association: The AGA offers multiple grants for research advancing the science and practice of Gastroenterology.
51. Wilson Ornithological Society Research Grants: The Wilson Ornithological Society Research Grants offers up to four grants of $1500 dollars for work in any area of ornithology.
52. The Obesity Society: The Obesity Society offers grants of up to $25,000 dollars to members doing research in areas related to obesity.
53. The Sjögren’s Syndrome Foundation: The SSF Research Grants Program places a high priority on both clinical and basic scientific research into the cause, prevention, detection, treatment, and cure of Sjögren’s.
54. The Melanoma Research Foundation: The MRF’s Research Grant Program emphasizes both basic and clinical research projects that explore innovative approaches to understanding melanoma and its treatment.
55. GRC - Run by the American Association of State Colleges and Universities (AASCU), the Grant Resource Center includes a database "customized to smaller institutions, and staff assistance," according to one user. A paid institutional membership is required for access.
56. IRIS - The Illinois Research Information Service is free for the University of Illinois (UI) community. Outside the UI system, a paid institutional subscription is needed for access.
57. SPIN - Run by InfoEd International, SPIN (the Sponsored Programs Information Network) claims to be the most widely used funding opportunity database in the world. An institutional subscription is required for access.
58. COS - Funding Opportunities. Community of Science claims the "largest, most comprehensive database of available funding," with 700 member institutions. Individuals can register free, but this won't get you access to the funding database.
59. ResearchResearch - Based in London, ResearchResearch provides an international option for people seeking research-funding programs. A paid subscription is required for access.

# install.packages('VennDiagram')
library(VennDiagram)

Second step: Load data

Add filepath if “catdoge.csv” is not in working-directory.

d <- read.csv("catdoge.csv")

Address of the bookmark: http://rstudio-pubs-static.s3.amazonaws.com/13301_6641d73cfac741a59c0a851feb99e98b.html

• January 20th, 2016 - New! Bpipe 0.9.9 released!
• Download latest, all
• Documentation
• Mailing List (Google Group)

Bpipe has been published in Bioinformatics! If you use Bpipe, please cite:

Sadedin S, Pope B & Oshlack A, Bpipe: A Tool for Running and Managing Bioinformatics Pipelines, Bioinformatics

Address of the bookmark: http://docs.bpipe.org/

CORE MODULES

Three modules make up the core engine for MCE.

MCE::Core

Provides the Core API for Many-Core Engine. The various MCE options are described here.

MCE::Signal

Temporary directory creation, cleanup, and signal handling.

MCE::Util

Utility functions for Many-Core Engine.

MCE EXTRAS

There are 4 add-on modules for use with MCE.

MCE::Candy

Provides a collection of sugar methods and output iterators for preserving output order.

MCE::Mutex

Provides a simple semaphore implementation supporting threads and processes.

MCE::Queue

Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.

MCE::Relay

Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.

MCE MODELS

The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.

MCE::Loop

Provides a parallel loop utilizing MCE for building creative loops.

MCE::Flow

A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.

MCE::Grep

Provides a parallel grep implementation similar to the native grep function.

MCE::Map

Provides a parallel map model similar to the native map function.

MCE::Step

Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.

MCE::Stream

Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.

MISCELLANEOUS

Miscellaneous additions included with the distribution.

MCE::Examples

Describes various demonstrations for MCE including a Monte Carlo simulation.

MCE::Subs

Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.

REQUIREMENTS

Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.

SOURCE AND FURTHER READING

The source, cookbook, and examples are hosted at GitHub.

• https://github.com/marioroy/mce-perl

• https://github.com/marioroy/mce-cookbook

• https://github.com/marioroy/mce-examples

SEE ALSO

MCE::Shared provides data sharing capabilities for MCE. It includes MCE::Hobo for running code asynchronously.

• MCE::Shared

• MCE::Hobo

Address of the bookmark: https://github.com/marioroy/mce-examples

Address of the bookmark: http://paintmychromosomes.com/

The goal of this tutorial is to run you through a demonstration of the command line, which you may not have seen or used much before.

All of the commands below can copy/pasted.

sudo apt-get update && sudo apt-get -y install python ncbi-blast+

wget ftp://ftp.ncbi.nih.gov/refseq/B_taurus/mRNA_Prot/cow.1.protein.faa.gz
wget ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/mRNA_Prot/human.1.protein.faa.gz

gunzip *gz
ls

head cow.1.protein.faa
head human.1.protein.faa

grep -c '^>' cow.1.protein.faa
grep -c '^>' human.1.protein.faa

head -6 cow.1.protein.faa > cow.small.faa

makeblastdb -in human.1.protein.faa -dbtype prot
ls

blastp -query cow.small.faa -db human.1.protein.faa

    blastp -query cow.small.faa -db human.1.protein.faa -out cow_vs_human_blast_results.txt
ls

less cow_vs_human_blast_results.txt

blastp -help

blastp -help | less

blastp \
-query cow.small.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 7

head -199 cow.1.protein.faa > cow.medium.faa

grep -c '^>' cow.medium.faa

blastp \
-query cow.medium.faa \
-db human.1.protein.faa \
-out cow_vs_human_blast_results.tab \
-evalue 1e-5 \
-outfmt 6 \
-max_target_seqs 1

Warning! This software is to be considered under development. Functionality and the user interface may still change significantly from one version to another. If you want to use this software, please stay up to date with the list of known issues:https://github.com/BinPro/CONCOCT/issues

Address of the bookmark: https://github.com/BinPro/CONCOCT

Address of the bookmark: http://seqmule.openbioinformatics.org/en/latest/

Samtools

Reading/writing/editing/indexing/viewing SAM/BAM/CRAM format

BCFtools

Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants

HTSlib

A C library for reading/writing high-throughput sequencing data

Samtools and BCFtools both use HTSlib internally, but these source packages contain their own copies of htslib so they can be built independently.

Address of the bookmark: http://www.htslib.org/