(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Bhubaneswar 751023

Advt No. 07/2016

Institute of Life Sciences (ILS), Bhubaneswar, an autonomous Institute of the Department of Biotechnology, Ministry of Science & Technology, Government of India engaged in advanced research invites applications from Indian nationals for the Ph.D. program. The main focus of the projects will be computational biology in the following areas.

S. No. Area of Research Principal investigator

1. Computational Cancer Biology Dr. Anshuman Dixit

2. Immunogenomics & Systems Biology Dr. Sunil Kumar Raghav

3. Chromatin remodeling and hematopoiesis Dr. Punit Prasad

Candidates are strongly encouraged to visit ILS webpage for detailed information, regarding the research activities of the above mentioned scientists.

Essential Qualifications:

(a) Eligibility: M.Sc., M.V.Sc., M.Pharm., M.S. Pharma. (with NET/GATE/GPAT/BINC/any other equivalent national level exam) or M.Tech with minimum of 60% marks (or equivalent grade point). Those awaiting final result may also apply.

Applications received after the last date will not be accepted. The envelope should clearly be superscribed with “Application for Ph.D. program (computational biology)”. Short-listed candidates selected for the interview will be published in the Institute website (www.ils.res.in).

Application Fees: Applicants except SC/ST candidates are required to send a non-refundable D.D. for Rs.100/- in favour of “Director, Institute of Life Sciences, Bhubaneswar” payable at Bhubaneswar along with duly filled-in application form by the date mentioned below. Director, ILS reserves the right to withdraw the procedure without assigning any reasons thereof.

Important dates: 

Last date of receiving applications: 24th June 2016 

Date of display of short-listed candidates and instructions on the Institute website: 30th June 2016 

Date of interview: The interview will be organized on 25th July 2016

Advertisement: https://www.ils.res.in/wp-content/uploads/2016/05/advt07-16.pdf

https://github.com/pditommaso/awesome-pipeline

Address of the bookmark: https://github.com/pditommaso/awesome-pipeline

More at https://github.com/neufeld/pandaseq

Address of the bookmark: https://github.com/neufeld/pandaseq

PEAR evaluates all possible paired-end read overlaps and without requiring the target fragment size as input. In addition, it implements a statistical test for minimizing false-positive results. Together with a highly optimized implementation, it can merge millions of paired end reads within a couple of minutes on a standard desktop computer.

More at http://www.exelixis-lab.org/web/software/pear

Paper: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3933873/

Address of the bookmark: http://www.exelixis-lab.org/web/software/pear

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

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

Canu is a hierachical assembly pipeline which runs in four steps:

• Detect overlaps in high-noise sequences using MHAP
• Generate corrected sequence consensus
• Trim corrected sequences
• Assemble trimmed corrected sequences

Read the documentation

New release https://github.com/marbl/canu/releases

Address of the bookmark: https://github.com/marbl/canu