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Statistics |
| Unique Visitors: 27 |
| Total Unique Visitors: 90413 |
| Visitors Out: 723 |
| Total Visitors Out: 1014 |
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| Papermaker: An easy way to validate scientific publication. |
| 2011-04-12 03:41:00 |
A well written scientific publication has high chance of getting through the peer review process. Research publication has to comply with standards concerning the document format, the use of language and the citation of prior work. Once the manuscript is written in loosely structured natural language by the researcher, the manuscript has to be validated for 1) Proper use of acronyms and their definitions. 2) Spellings 3) GO and MeSH terms 4) References Papermaker receives a scientific manuscript via web interface, analyses the publication, evaluates consistency parameters and interactively delivers feedback to the author. It performs the task of spelling checks, analyses the proper use of acronyms and their definitions. Further it provides Gene Ontology (GO) and Medline Subject Headin...
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| Interactive software tool for optimal sequence alignments with dynamic programming. |
| 2011-04-11 02:28:00 |
Dynamic programming (DP) is an optimizing strategy commonly used in various discipline in science. It is widely used in biology to calculate optimal alignment between pairs of protein or DNA sequences. DP is so important, that it is core of many software applications available today for sequence analysis. DP algorithm is essential topic in many undergraduate and graduate bioinformatics course. Although simple in formulation, DP is not that easy for students to learn. Sequence alignment teacher (SAT) is a simple software, which interactively calculates the DP matrix in real time. Also SAT visually illustrates the consequence of tweaking the various parameters of the algorithm. 1) The user can visualize and modify the values in the similarity matrix and the gap opening/exten...
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| Setting up a Citation Alert Service |
| 2011-03-27 05:02:00 |
The number of research publication added everyday to the database is increasing and keeping track of the recent developments in the field may be difficult task.A citation alert notifies you by e-mail whenever a article you choose has been cited by a new article when it is added to the database. Pubcrawler Pubcrawler is a free alerting service that searches daily updates to the NCBI Medline (PubMed) and GenBank databases. Pubmed automatically searches the pubmed and emails you the results. PubMedAlertMe- PubMedAlertMe is a Windows-based software system for automatically receiving e-mail alert messages about recent publications listed on PubMed. Biomail BioMail is a small web-based application for medical researchers and biologists. It is written to automate searching for recent scient...
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| Science blogger vs Scientist blogger: The debate continues… |
| 2011-03-07 07:53:00 |
This issue has been covered by many posts, probably many times. Let’s analyze the view of prominent blog authors on this topic. Most of the science blogs that we see today are not necessarily by professional scientist. So you have the science blogs by Writers/authors/ Journalists who may have experience and a degree in science, so called type I bloggers. And there are blogs by researchers /scientist who from their busy schedule take time off to write science for general audience (TypeII). The post by “Highly Allochthonous” draw our attention to two research papers in the journal “Nature” on the affects of human-caused global warming on extreme precipitation events. Here are the first lines of each of those features. “The varying distribution of fresh water across the globe, ...
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| Who is citing whom: A comparison of popular citation tracking tools. |
| 2011-02-26 04:37:00 |
Researchers use citation tracking tools to see how often their published article is cited. This is one way to assess the impact of your scientific work and also a method to find the most influential article for a particular research topic. Web of science from Thomson scientific was the only source to get citation related information until 2004. However with the launch of Scopus from Elsevier and Google scholar from google, a user has options when it comes to citation tracking. Among the three citations tracking service mentioned above only Google scholar has free access. Understanding how citation tracking tool respond to keyword query is important when it comes to finding relevant article for particular research topic. Among the three tools, Scopus provides wider journal range, bo...
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| Academic Search Engine Optimization |
| 2011-02-21 11:41:00 |
Websites have to be search engine friendly and easily accessible for crawling and indexing. The process of making the website or blog search engine friendly is called as search engine optimization (SEO). All webmasters are familiar with the term SEO. However for researchers and academician SEO may not be a familiar term. I was unaware about use of SEO in academics, and always ignored it while writing research publication until recently. I will introduce you to the concept of academic search engine optimization. “Academic search engine optimization (ASEO) is the creation, publication, and modification of scholarly literature in a way that makes it easier for academic search engines to both crawl it and index it.” Unlike website SEO, ASEO is different in following ways; On...
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| Molecular Editor |
| 2011-02-13 23:09:00 |
A molecule editor is a computer program for creating and modifying representations of chemical structures. Two dimensional molecular editors are used to to generate two-dimensional (flat) representations of molecules and chemical reactions that can be used as illustrations or for querying chemical databases. While three dimensional molecular editors are used to build molecular models. Most molecule editors use proprietary file formats, but most can read and write several file formats, including SMILES. The file created by molecular editor can be displayed in a molecular graphics tools.
Some commonly used molecular editor programs are
ACD/ChemsketchAscalaph ISIS/DrawMarvinSketch
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| List of free molecular viewer |
| 2011-02-11 07:35:00 |
Given here are list of freely available moleculer viewer with outstanding features. Invidualy comparing the features of each of these programs are realy too much of work for me. Most of these programs have general features including standard representation ( ribbon, ball and stick, space filling etc) and various coloring features.
Cn3DIntegrated sequence alignment view; embeddable
Chime Widely used; structure editing; electrostatic maps; embeddable
Chimera Popular; integrated sequence alignment viewer (EDM, MD)
DS Visualizer Free version of Accelrys’s powerful viewer/editor program
ICM-Browser High quality images; integrates with sequence alignment viewer
IMOD Tomogram al...
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| Molecular graphics overview |
| 2011-02-11 01:32:00 |
Molecular Visualization is the process of interpreting visual images of molecules. Molecular graphics refers to a technique for the visualization and manipulation of molecules on a graphical display device. Advancement in computational science has changed the way molecular structures are presented and displayed. In this section I will discuss about various graphical visualization and manipulation tools used in chemical and biological research.
All molecular graphics program reads a particular molecular file format and then translates these into a picture according to the representations specified. Besides moleular graphics programs can also be used to map and display molecular properties.
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| Scientific writing in MS word |
| 2011-02-07 06:30:00 |
The MS word guide provided here gives information useful when writing a research article, report or PhD thesis using MS Word. I am not in any way promoting the use of Microsoft word. As discussed in the post latex Vs word recommending a single document system is difficult. And in future post I would attempt to include information about other alternatives like open office and latex. The article given below is written by Birgitta Malmfors is useful for begineers
Scientific writing in word
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