Programming languages slated for history's dustbin of dead tech?
Here are the dead and dying languages
1) Perl - because it's a "piecemeal" language with features pile atop one another
2) Ruby - because its difficult to learn if you know C
3) Visual Basic.Net - because C#
4) Adobe Flash & AIR - because iPhone
5) Delphi Object Pascal - because it isn't well-supported
1) Perl - because it's a "piecemeal" language with features pile atop one another
2) Ruby - because its difficult to learn if you know C
3) Visual Basic.Net - because C#
4) Adobe Flash & AIR - because iPhone
5) Delphi Object Pascal - because it isn't well-supported
Labels:
language
Journal selection tools
The Journal Selectors use semantic technology to help you quickly choose
the open access journal that is right for your manuscript. Matches to a
journal are based on already published articles that are similar to
your research, allowing you to match to similar articles from a database
of over 300,000 articles.But based on my personal experience,I have listed the free selection tools in order of their relative accuracy .
1.Edanz Journal selector
http://www.edanzediting.com/journal_selector
2.Elselvier journal finder
http://journalfinder.elsevier.com/
3.JANE
http://www.biosemantics.org/jane/
4.Springer
http://www.springer.com/gp/authors-editors/journal-author/journal-author-helpdesk/preparation/1276
5.Springer-Open
http://www.springeropen.com/authors/authorfaq/findout
6.Biomed central tool
http://www.biomedcentral.com/authors/chooseajournal
The one by wiley-balckwell is so pathetic that I didn't mention it:P
coming soon:
Journal selector at
http://cofactorscience.com/journal-selector
if you know of any other good tool that I 've missed,feel free to add it in the commnets section:)
1.Edanz Journal selector
http://www.edanzediting.com/journal_selector
2.Elselvier journal finder
http://journalfinder.elsevier.com/
3.JANE
http://www.biosemantics.org/jane/
4.Springer
http://www.springer.com/gp/authors-editors/journal-author/journal-author-helpdesk/preparation/1276
5.Springer-Open
http://www.springeropen.com/authors/authorfaq/findout
6.Biomed central tool
http://www.biomedcentral.com/authors/chooseajournal
The one by wiley-balckwell is so pathetic that I didn't mention it:P
coming soon:
Journal selector at
http://cofactorscience.com/journal-selector
if you know of any other good tool that I 've missed,feel free to add it in the commnets section:)
Labels:
publishing,
semantic web
Putting QR code in conference poster
New piece of tech-innovation that I came across today, Putting QR codes on your poster for smartphone users.They are simple and very versatile.But among many things that one can do with QR code, one is that there are so many things that one could do with a QR code that the temptation would be strong to do all
of them. The poster should not look like some mysterious stamp
collection. Pick one, maybe two, things you want to do with a QR code
and do them well.I tried this free link for this purpose and it gave good results.
http://zxing.appspot.com/generator/
http://zxing.appspot.com/generator/
Labels:
code
OMICs tool directory
It is important to keep abreast of the continuous development of NGS and array software and avoid redundancy. OMICtools
provides an overview of more than 2200 tools. All tools have been
classified and detailed information provided. By making this resource
available, we aim to help both bioinformatics experts and other
researchers find appropriate tools for their needs. The directory can
also be used by life scientists as an educational or quick-reference
support.
It is a free metadatabase for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, MS, NMR). OMICtools is expected to serve as a useful didactic resource not only for bioinformaticians, but also for experimental researchers and clinicians.
http://omictools.com/
It is a free metadatabase for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, MS, NMR). OMICtools is expected to serve as a useful didactic resource not only for bioinformaticians, but also for experimental researchers and clinicians.
http://omictools.com/
Labels:
bioinformatics,
omics,
software
Hemingway to improve writing
I recently found this little gem of a web app that analyzes the clarity of your writing. Hemingway
highlights long, complex, and hard to read sentences. It also
highlights complex words where a simple one would do, and highlights
adverbs, suggesting you use a stronger verb instead. It highlights
passive voice (bad!), and tells you the minimum reading grade level
necessary to understand your writing.
When I pasted in some text from an abstract I submitted to ASHG years ago it showed me just how terrible and difficult to understand my scientific writing really is. My abstract text, which should have been hard-hitting and easy to understand at a glance, required a minimum grade 20 reading level. The majority of my 14 sentences were very hard to read and littered with too many adverbs, complicated words, and several uses of passive voice. (I still got a talk out of the submission, so maybe we as scientists enjoy reading tortuous verbiage...).
http://www.hemingwayapp.com/
When I pasted in some text from an abstract I submitted to ASHG years ago it showed me just how terrible and difficult to understand my scientific writing really is. My abstract text, which should have been hard-hitting and easy to understand at a glance, required a minimum grade 20 reading level. The majority of my 14 sentences were very hard to read and littered with too many adverbs, complicated words, and several uses of passive voice. (I still got a talk out of the submission, so maybe we as scientists enjoy reading tortuous verbiage...).
http://www.hemingwayapp.com/
Labels:
language,
publishing
Stein was right in saying Bioinformatics is a tool,not a field...
He gave the ultimatum on the death of this field in 2003 and in Pakistan where not much NG science is taking place,this has been proved. No jobs for those who specalize in bioinformatics alone.They are considered a half-and-a-half.Not accepted into biology as not enough of a biologist and not accepted into CS disciplines as not specialist of that field.
I agree with Stein that "It is a tool and not a scientific discipline. Tools get absorbed into the greater disciplines. There are examples of disciplines defined by a problem domain contrasted with services defined by tools.
Robust scientific disciplines are often defined by a problem domain. For example, a development biologist studies the development of multicellular organisms using what ever tools are at hand. They aren't defined by the tools they use. A pharmacologist studies the interactions of chemicals with physiological properties. Similarly, physicists aren't defined by their tools; they study the nature of matter and energy.On the other hand, services are defined by tools and they are often time-limited. For example, a microscopist knows how to use microscopes. Now that a microscope is a ubiquitous tool you won't find many specialists in this area. While a pharmacologist has a problem domain, a pharmacist knows how to compound medicines and fill out regulatory paperwork. There are fields that cross over. Stein offered molecular biology as an example of a scientific discipline that has transitioned to a service.
Most of the biologists are bioinformaticians now.It is too central to biology to be left out to specialized bioinformaticians.Colleges and universities should inculcate bioinformatics in the core curriculum.
Bioinformatics was a tool (or set of tools) like microscopy, used to answer complex biological questions. "
Bioinformatics is just one way of studying biology. Whether you think of bioinformatics as High Throughput Biology, Integrative Biology, or Large Data Set Biology, fundamentally Stein argues that bioinformatics is biology.It is not strange when biologists never touch goosh: body parts, liquids.... because they're studying life. Biologists like Ernest Mayer can sit in his office and look at other people's data and develop theories of selection.
Biologists should take programming classes.
Computer has become a central tool for biology like the microscope or the centrifuge. Being able to produce your own software for data analysis should be part of the undergraduate and graduate curriculum. In answer to a related question about computational biology, Stein answered that "it is algorithm development. It is a specialized discipline. I think it's a branch of CS.
Stein has some simple advice for how you make it in bioinformatics:
I agree with Stein that "It is a tool and not a scientific discipline. Tools get absorbed into the greater disciplines. There are examples of disciplines defined by a problem domain contrasted with services defined by tools.
Robust scientific disciplines are often defined by a problem domain. For example, a development biologist studies the development of multicellular organisms using what ever tools are at hand. They aren't defined by the tools they use. A pharmacologist studies the interactions of chemicals with physiological properties. Similarly, physicists aren't defined by their tools; they study the nature of matter and energy.On the other hand, services are defined by tools and they are often time-limited. For example, a microscopist knows how to use microscopes. Now that a microscope is a ubiquitous tool you won't find many specialists in this area. While a pharmacologist has a problem domain, a pharmacist knows how to compound medicines and fill out regulatory paperwork. There are fields that cross over. Stein offered molecular biology as an example of a scientific discipline that has transitioned to a service.
Most of the biologists are bioinformaticians now.It is too central to biology to be left out to specialized bioinformaticians.Colleges and universities should inculcate bioinformatics in the core curriculum.
Bioinformatics was a tool (or set of tools) like microscopy, used to answer complex biological questions. "
Bioinformatics is just one way of studying biology. Whether you think of bioinformatics as High Throughput Biology, Integrative Biology, or Large Data Set Biology, fundamentally Stein argues that bioinformatics is biology.It is not strange when biologists never touch goosh: body parts, liquids.... because they're studying life. Biologists like Ernest Mayer can sit in his office and look at other people's data and develop theories of selection.
Biologists should take programming classes.
Computer has become a central tool for biology like the microscope or the centrifuge. Being able to produce your own software for data analysis should be part of the undergraduate and graduate curriculum. In answer to a related question about computational biology, Stein answered that "it is algorithm development. It is a specialized discipline. I think it's a branch of CS.
Stein has some simple advice for how you make it in bioinformatics:
- Learn biology. Investigate the problem domain for bioinformatics.
- Pick a problem that interests you. Don't just follow where you think the hot topic is or what seems to be an easy problem. Consider what you are willing to spend the next decade or two or the rest of your life working on.
- Know your tools. Don't treat your tools as black boxes. Understand how they work and what their limitations are. With a microscope you don't need to know optics, but you should know something about light paths, magnification, and resolution. Don't be afraid to use non-computer tools. Don't find the problems that fit your tools.
- Don't be ghettoized. If you expect to be a scientist and to be doing research then don't come in just to perform services to apply your tools to other people's problems. If you want to write software and provide a service, that's great but do so deliberately.
- Do it because you love it.
Biologists are all bioinformaticians now.
Biologists are all bioinformaticians now.
Biologists are all bioinformaticians now.
Labels:
bioinformatics,
omics
Bioinformatics Periodic Table
Eagle's Elements of Bioinformatics is an interesting colourful and dynamic periodic table bringing together all the tools in each category of bioinformatics software so that end-users can find all the information in one place.
For example, someone looking for an aligner might use the table to review the options available before making the choice most appropriate to their project. Someone already using an aligner but having problems with it might use the table to identify suitable alternatives.
The original version of the table had only genomics and sequence bioinformatics tools, but we are steadily expanding it to cover other areas such as proteomics, biostatistics, metabolomics, etc.
The table divides all tools into categories by function and licence. The function groupings are colour-coded, and the licence groupings are represented by separation into dedicated areas. We don't list each individual licence, but instead allocate a general category of licence to each tool - completely free, free for academics only, or commercial/restricted.
The categories are listed at the top. Hover over a category to highlight all tools that fall into it.
Each tool can be hovered over to bring up more information including, where available, and a link to the tool's homepage (click on the two-letter abbreviation to be taken there).
Interactive version available at : http://elements.eaglegenomics.com/
source:http://elements.eaglegenomics.com/elements-about.html
Labels:
bioinformatics
Gene structure prediction tools
Links to bioinformatics resources designed to predict the structure of protein coding genes in genomic DNA sequences are given below:
1. http://genome.cbs.dtu.dk/services/HMMgene
2. Procrustes predicts gene structure using protein homology (Gelfand et al.,
1996)
3.Genewise - part of the Wise2 package: http://www.ebi.ac.uk/Wise2/
4.http://gsds.cbi.pku.edu.cn/
Labels:
bioinformatics,
software
Horizontal gene transfer predictor tools
Some of the bioinformatics tools for this purpose are:
1)HybRIDS (Hybridisation, Recombination, Introgression and Dating Software). It is a bioinformatics tool designed to visualize the signal of recombination (and genetic introgression, horizontal gene transfer) in DNA sequence data present in large (multiple kb) contigs and whole genome sequence data of three or more individuals. It reports several summary statistics of these events, including breakpoint positions, number of SNPs, and it estimates the age of the recombination event. HybRIDS can also be applied to analyse smaller amplicons.
HybRIDS has a user-interface, and it is simple and relatively fast to run. The output of HybRIDS aims to direct the user to more computationally-intensive phylogenetic and population genetic analyses, e.g. to confirm the recombination events with multiple algorithms present in RDP3 (Martin et al. 2010), and/or date the divergence of the recombination blocks in a Bayesian framework, e.g. in BEAST (Drummond et al. 2012).
The analysis with HybRIDS consists of the following three-steps:
1. Load nucleotide data in FASTA format into the R environment using the user interface.
2. Analyse the sequence similarity of all possible sequence triplets with a sliding window approach.
3. HybRIDS then detects recombination blocks and calculates summary statistics for each recombination block (i.e. number of SNPs, breakpoint positions, length of recombination block, the probability that sequence similarity is caused by mutations rather than by recombination). HybRIDS also draws graphs of contigs illustrating the location of recombination blocks relative to base position, and it estimates the mean (5-95%CI) coalescence time of each recombination block, and it thereby dates each recombination event.
A beta version of HybRIDS is available from http://www.norwichresearchpark.com/ourresearch/researchgroups/elsa/software/hybrids.aspx
2.A webserver for this purpose can be accessed at: http://www.bioclues.org/horigene/predict.php
3.Another webserver combining three tools can be accessed at: http://bioinformatics.publichealth.uga.edu/SpeciesTreeAnalysis/
Labels:
bioinformatics,
phylogenetics,
software
Influential Authors in microbial informatics
I'm into microbial informatics these days and keep bumping into papers of these scientists often....
(Source:Google citation index)
Jennifer WortmanDirector, Microbial Informatics, Broad Institute
Verified email at broadinstitute.org
Cited by 35417
Torbjørn RognesDepartment of Informatics, University of Oslo and Department of Microbiology, Oslo
Verified email at ifi.uio.no
Cited by 2692
Head Bioinformatics Centre, CSIR Institute of Microbial Technology, Chandigarh, India
Verified email at imtech.res.in
Cited by 5469
Kathleen Marchal… and Molecular systems, KULeuven; Dept of Plant Biotechnology and Bioinformatics, Ghent …
Verified email at psb.ugent.be
Cited by 4720
Samuel ChaffronPost-doc in Microbial Systems Biology and Bioinformatics, VIB and VUB Brussels
Verified email at vub.ac.be
Cited by 2391
Microbial Genomics and Bioinformatics, Karlsruhe Institute of Technology
Verified email at kit.edu
Cited by 338
Labels:
bacteria,
bioinformatics,
microbiology
Word!
While I appreciate biology from a purely scientific standpoint, I strongly believe research is useless if you can't communicate it. There's a great quote by Jules Poincaré that says: "Science is facts; just as houses are made of stone, so is science made of facts; but a pile of stones is not a house, and a collection of facts is not necessarily science." In my mind, what turns facts into science is the integration of research into society, whether for purely educational purposes or society's benefit, and that the key to that is communication. That's why I decided to start a science blog in 2008. As a scientist, I really believe that it is my responsibility to engage non-scientists and the public in general in my endeavors to give my work meaning.
Scientists already share what we do with each other. That's what journals are for. I wanted to share what I loved with everyone, not just my like-minded peers. I feel it is important to take jargon-filled scientific publications and break them down in such a way that everyone can understand what is being studied and why it is important. In modern media, science is only talked about if it can be sensationalized. So-called "real" journalists seem to think experiments are only worth mentioning if they can be summed up in a catchy but untrue headline or are controversial. But every day I read papers no one hears about that are just so.... *cool*. Science is unbelievably cool, and I blog because I think that maybe if the rest of the world saw science how I do, they would think it was pretty cool, too. And maybe if they did, there would be more scientists doing unbelievably cool stuff for me to blog about!
(via scienceblog feed)
How Lab Politics eat you and your project:(
Most of the posts I come across are about supervisors and their bad attitude which is no doubt a big problem and hinders progress, makes you mad and destroys you and your career. In addition to that, even if your supervisor is good and Lab fellows are not, it's equal damage. So today's post is about that...
Generally, the present work, when you start is new to you and you will ask questions from seniors and also try to help lab-mates with their work so that your could learn and earn good name, but if request you make to them to teach you is met with hostile remarks, you are in wrong place. Unfortunately, nothing much can be done about this hell at official level. Highlighting them would make you more vulnerable if you are not with someone to stand at your back, teach you to manipulate them and sometimes supervisors seem to aggravate the situation and mostly they don't care. Some inside people will fan the situation for fun. I don't know about European countries but it is a typical mind set here, leg pulling and make one a target for fun. I have seen Labbies even yell at new comers for no reason, just to make sure that they are considered more knowledgeable, more powerful and more established.
Communication is sometimes indirect, sometimes direct but mostly unclear, controlled, and often manipulated. Breakage/equipment failure is not reported and one is made scapegoat in front of the supervisor/management...:(
You are kept isolated from their company and in the dark about what is going on.They back stab you in front of supervisor/management.
Your supervisor kind of blames you for your attitude in most cases!
This definitely makes one mad due to unfair situation, there is a limit for misunderstanding and conflict.
Best solution is to change Lab. You deserve more than you are getting. Don't leave hope and let yourself be vulnerable.The damage done to your mental and other health as a consequence would be far greater as compared to the six months or a year you waste while searching for some other proper Lab. Please don't play with your life.
I seriously think that there should be an International body governing/aiding all scientific activity and serious Laws to protect the victims and punish the culprits.
Generally, the present work, when you start is new to you and you will ask questions from seniors and also try to help lab-mates with their work so that your could learn and earn good name, but if request you make to them to teach you is met with hostile remarks, you are in wrong place. Unfortunately, nothing much can be done about this hell at official level. Highlighting them would make you more vulnerable if you are not with someone to stand at your back, teach you to manipulate them and sometimes supervisors seem to aggravate the situation and mostly they don't care. Some inside people will fan the situation for fun. I don't know about European countries but it is a typical mind set here, leg pulling and make one a target for fun. I have seen Labbies even yell at new comers for no reason, just to make sure that they are considered more knowledgeable, more powerful and more established.
Communication is sometimes indirect, sometimes direct but mostly unclear, controlled, and often manipulated. Breakage/equipment failure is not reported and one is made scapegoat in front of the supervisor/management...:(
You are kept isolated from their company and in the dark about what is going on.They back stab you in front of supervisor/management.
Your supervisor kind of blames you for your attitude in most cases!
This definitely makes one mad due to unfair situation, there is a limit for misunderstanding and conflict.
Best solution is to change Lab. You deserve more than you are getting. Don't leave hope and let yourself be vulnerable.The damage done to your mental and other health as a consequence would be far greater as compared to the six months or a year you waste while searching for some other proper Lab. Please don't play with your life.
I seriously think that there should be an International body governing/aiding all scientific activity and serious Laws to protect the victims and punish the culprits.
Lab confessions
Hahahaha!
You think I 'm going to confess here?
Not in a million years,but your effort of opening this tab shouldn't go to waste entirely so here is a piece of entertainment for you,relevant to the topic:)
A little while ago,someone on twitter started the #LabConfessions trend. Loads of scientists from all around the world tweeted the absurdities committed by them in Lab.Some of them are compiled here for your enjoyment.You can add to the list in the comments section:)
Happy reading:)
1.The last sentence on the last page of my PhD thesis says 'Well that's what I think anyway". Nobody's noticed yet.
2.I wet my shorts right before my first conference talk of my career
3.The worst letter from an editor: "Unfortunately, I must accept the paper for publication because three reviewers said so."
4.As a postdoc, I discovered that ciliates are phylogenetically closer to cows than to one another. Gave up wet science.
5.I saw a grad student jump into a bush to avoid my advisor and I told
6.I published a techniques paper just so I could say "arse" in presentations at conferences.
7.I once gave terrible honours student tubes of water to pipette rather than valuable cDNA for PCR. Did real expt myself
8.I often forget to take the lid off Petri dishes when pouring agar plates
9.I often label wrong side of petri plates b4 pouring agar
10.Once stuck my Prof to the toilet floor by throwing liquid nitrogen under the cubicle door
11. Interesting,back then in my first days at the lab, I was given pH strips with a tiny comparison chart to check the pH of my buffer. Instead of dipping the clear red strip, I dipped the whole comparison chart in the buffer thinking the specific color change will occur at one of the pH points on it. My PI entered the room and was looking at me. Felt bad the whole day coz he thought I knew and I screwed up.....with a basic pH test, still feel bad now that I've remembered.
12. I 'm not positive but I might have ruined the lab manager's Saturday night by misreading the thermometer.I was working late, and no one else was around, and upon opening the -20 freezer I happened to check the temperature and noticed it was well above -20. I panicked. I ended up calling the PI and the lab manager, and the lab manager drove 30-45 minutes from home to get to the lab in case we needed to move all the stuff out to other freezers. But by the time she arrived, the thermometer was pretty close to -20 again. I don't know if it's because I had been opening and closing it a lot while I was working, or because I misread the thermometer in Fahrenheit instead of Celsius (why would a Science Thermometer even have Fahrenheit gradations?), but I noticed Fahrenheit was the side that was currently exposed.
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