More at http://bioinf.spbau.ru/quast

http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/early/2013/03/09/bioinformatics.btt086.long

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/

http://compbio.cs.toronto.edu/prism/

Address of the bookmark: http://compbio.cs.toronto.edu/prism/

1. Learn and get updated

Some of the bad biological programmers only learn new technical or non-technical things when it’s absolutely necessary. The good biological programmers learn new technical skills proactively. But great biological programmers not only learn new technical skills on their own but also learn non-technical skills, and have an open mind to sources of knowledge that others may shut out.

In other concrete term, the bad biological programmer learn Perl's regular expression when they started a project on comparative genomics; the good biological programmer learned it a year before because it looked interesting; and the great biological programmer also read about the BioPerl packages, genomics, DNA string, genomic theories, or some similar course of study so that they could understand the results and explain it biologically.

2. Not a merely coder!!!

I often encountered with biological programmer who call themself a hard-core computer programmer and avoid biology. I can almost guarantee that if you are one of them then you are not doing research but merely writing "dry" codes.

According to my supervisor most of the computational biologist, don't know what they are doing biologically. Even they struggle to explain their own programs output and results. Therefore, It is highly advisable to learn basic of biology which can assist you to explain the result and understand your discovery. Always remember you are a researcher not a coder.

3. Be Social with biologist

The computational biologist spends most of the time in from of computers, writing codes. They always think their job is to produce working codes, not technical research perfections. But, they are completely wrong. You should not forget that apart from your computational skills you also need some biologist, other than your supervisor, to explain and make you understand the complex biological mechanism.

I highly recommend your to interact with biotech researchers and learn how do they explain their one graph (which they generally produce after one year of work) biologically. Remember, the origin of your research project is complex biological phenomenon, which is more complex than that of your limited programming rules.

4. Do not search, research for answers

Researching for answers means more than typing several keywords into a search engine or posting a question at Stack Overflow or the BioStars forums. I have entered problems into search engines that generate no results, and every question I posted on Stack Overflow or the BioStars forums never got anything resembling an answer, yet I solved the issues and moved on. I’m not a magician — I just know how to find answers or discover root causes.

Many problems are situational, and if you depend on search engines and forums, you can waste a lot of time going down a rabbit hole and possibly never getting a solution. Learn to perform root cause analysis, learn enough about the underlying system to look for other clues and solutions, and learn to take a long distance view of an issue before deep diving into it.

5. Love and defend your research

You cannot rise to the top in this research profession without loving your work. There are some very good “it’s just a job” biological programmers (I’ve been one at times), but if that is your outlook, you won’t be willing to do whatever it takes to succeed. This idea gets a lot of folks in a huff, because they feel it is a personal insult. “I’m a good programmer, but I have other priorities and can’t make work my life.” I understand completely; I have other priorities too. As much as I hate to say it, when I am passionate about my work, I am willing (though not eager) to abandon my other priorities to finish the job. It is not an insult to say that if you aren’t willing to pull out all the stops you can’t be the best, it is a fact.

You must be passionate about more than programming — you must also be excited about your research, the tools and technology you are using, and so on. I have seen very good and even great biological programmers operating at mediocre levels because something was not a good fit, such as they hated the project or were using a technology they disliked. Therefore, like your research project and get excited about your discoveries. You have not only to discover but also defend your finding with scientific words.

Thanks to all of you for reading.

MEME Suite software development; gene expression; mathematical modelling; gene regulation and transcription

Specialization:
Pattern recognition and modelling in computational biology

Link @ http://www.imb.uq.edu.au/tim-bailey

Applications are invited for the STUDENTSHIP and TRAINEESHIP vacancies to carry out project/research work in the DBT - Bioinformatics Infrastructure Facility with consolidated stipend of Rs.5,000/- per month.

Essential Qualification

Student Trainee: Those who have completed M.Sc., Bioinformatics/Biophysics/Life sciences or Pursuing M.Tech., Bioinformatics/Biotechnology

Duration : 3-4 Months

Student Trainee: Those who are pursuing M.Sc Bioinformatics/Biophysics/ Life sciences/others

Duration : 2-3 Months

Mail your CV on or before 25th November 2013 to shirai2011@gmail.com and hard copy to "Dr. D. Velmurugan, Professor & Head, CAS in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025". Also, the applicants are requested to attend the interview on 29th November, 2013 at 11 A.M.

Advertisement:

www.unom.ac.in/uploads/announcements/bifadvertisement_20131114080003_23240.pdf

Genomes and genomics:

Bioinformatics and Genomics:

Structural genomics tutorial:

Comparative Genomics Tutorial:

GENOME TUTORIAL:

Tools and resources for identifying protein families, domains and motifs

Bioinformatics Tools 
Tips, Tutorials, and Terminology for Using Selected Resources in Genome Database Guide:

A Web-Based Comparative Genomics Tutorial for Investigating Microbial Genomes:

Free Online Tutorials Teach Anyone How to Use Genome Databases:

Circos to create concise, explanatory, unique and print-ready visualizations of your data:

Genomics and Comparative Genomics Learning Module:

Computational Challenges in Comparative Genomics

A Tutorial:

A Comparative Genomics Resource for Grains:

PLAZA: A Comparative Genomics Resource to Study Gene and Genome Evolution in Plants:

VISTA:

Software for Genomics

1. Artemis Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.
2. Chromas It will display and prints chromatogram files from ABI automated DNA sequencers, and Staden SCF files which the analysis programs for ALF, Li-Cor and Visible Genetics OpenGene sequencers can create.
3. Glimmer A system for finding genes in microbial DNA, especially the genomes of bacteria and archaea.Glimmer (Gene Locator and Interpolated Markov Modeler) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DN
4. Glimmer HMM A fast and accurate gene finder based on a GHMM architecture, developed specifically for eukaryotes. It incorporates splice site models adapted from the GeneSplicer program and uses interpolated Markov models for evaluating the coding regions.
5. Glimmer M A gene finder derived from Glimmer, but developed specifically for eukaryotes. It is based on a dynamic programming algorithm that considers all combinations of possible exons for inclusion in a gene model and chooses the best of these combinations. The d
6. MUMmer MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form.
7. pDRAW pDRAW32 is being developed as a free time hobby project. It is far from finished, but as it has reached a point where it could be helpful for many labs, it is now available to the scientific community.
8. Sequin Sequin is a stand-alone software tool developed by the NCBI for submitting and updating entries to the GenBank, EMBL, or DDBJ sequence databases. It is capable of handling simple submissions that contain a single short mRNA sequence, and complex submissio
9. Staden The Staden Package consists of a series of tools for DNA sequence preparation (pregap4), assembly (gap4), editing (gap4) and DNA/protein sequence analysis (spin).

For more software @ http://bioinformaticsonline.com/bookmarks/view/926/list-of-popular-bioinformatics-softwaretools

The most common newbie questions are:

Should I try to use these free open source programs?  Why are we not trying GUI software for computational analysis? Should I use commercial bioinformatics programs/software?”

1. Let’s be open

We generally think free and cheap are useless. But this concept is not applicable when we discuss open source software. Mostly, the bioinformatics software is developed by highly competitive biological programmers who believe in open sharing of knowledge. They come under Open Bioinformatics Foundation or O|B|F which is a non-profit, volunteer run organization focused on supporting open source programming in bioinformatics. The best part about open source tools/software is that they’re free to download the source code and read exactly what the program does. If you are so inclined, you can view all of the parts of the program and see the logical flow of the pipeline. In addition, open source makes an excellent learning tool for any beginning bioinformatician. Moreover, you can modify existing open source programs to deal with cutting-edge problems or to customize your pipeline. Apart from your computational and analysis work, most of the reviewer also prefers the open source based results so that they can validate the results if validation required.

2. Code headache

As a bioinformatician you are supposed to know the basics of programming languages, and if you are not good at it, then please learn it as soon as possible because you are not a bio-analyst but biological programmers. The open source programs usually lack dedicated service and support teams (often because they were the product of an overworked doc/postdoc!) so you are responsible for troubleshooting your own errors most of the time. We commonly receive the HELP email to support and assist to setup the pipeline; you can also find this kind of request on any QA forum. I personally believe this coding horror brings the biggest downside of open-source programs; where you need some programming skills in order to implement the program in your pipeline. But, if you are not able to fix the pipeline and modify the open source code according to your requirements them you should re-think on your bioinformatician name tag!!!

3. Dive into the codes

Some of the biologist turn bioinformatician says “if you can do the same thing with commercial software then why to get migraine with weird codes”, well this statement looks to me that guys are keen to learn swimming but still don’t like to get wet. If you are still using paid software and doing your work by customer support and clicking some of the well-designed GUI button then perhaps you are not interested in learning and trying new and challenging bioinformatics works. You are missing the basic flavour of bioinformatics. Let’s dive into the coding world, I am sure your will enjoy it. I recommend your to swim freely in code’s sea, and enjoy the journey; do not merely watch it from the outside.  

4. Paid does not mean better

The bioinformatics company which are specializes in bioinformatics solutions develop well designed/packed, user friendly software by using a large number of specialised scientist, programmers and support staff. They also provide good services to accomplice your biological analysis work. This means that if you hit a ‘snag’ with your data, help is likely only a phone call away! These companies price their products competitively against the cost of a dedicated bioinformatician. You may be able to afford the program, but not the additional staff! Additionally, most of the functionality that you need in your analysis is already coded into the program. Need to plot a graph? Just click this button right here. It is that easy. But, as a bioinformatician this is not generally well encouraged approach in biological analysis work, because the software is not available to everyone and your data can’t be validated. Moreover, there is very less chances that anyone will repeat your work or love to do similar kind of research (because not all the labs in the world are rich like yours).

5. Take a caution

In biological analysis work, in which you deal GB/TB of data are having maximum chances of getting errors, so please be careful and always cross check your data before coming to any conclusion. Even an error in two line code can alter your entire analysis and display weird results. Some of the scientist blindly believes on commercial software, which is entirely wrong. Using proprietary tools does not absolve you of the need to actually read and research the type of analysis that you are doing. This is particularly true in the case of genome assembly and annotation.

At the end, I would like to tell only one think that open source solutions allows you to do more cutting edge analysis than the commercial tools. So let’s go for it.

Disclaimer:

This is my personal view. I have nothing to do with any company or open source community. The views expressed on these pages are mine alone and not those of my current/past employers. I do reserve the right to remove comments left by spammers or off-topic comments.