http://molvis.sdsc.edu/visres/index.html#c-rtu
World Index of
Molecular Visualization Resources
www.molvisindex.org
freeware:
http://molvis.sdsc.edu/visres/molvisfw/titles.jsp
http://www.cgl.ucsf.edu/chimera/download.html
Online Services headline animator, feedBurner
Friday, May 23, 2008
Thursday, May 22, 2008
Wednesday, May 21, 2008
Atlas mouse and software
A variety of 2D data is presented by a number of world
wide web sites: the High Resolution Mouse Brain Atlas
(http://www.hms.harvard.edu/research/brain), the Edin-
burgh Mouse Atlas Project (http://genex.hgu.mrc.ac.uk),
and the Mouse Brain Library (Rosen et al., 2003)
(http://www.mbl.org).
Software packages are available for visualizationof different data modalities and brain alignment
(the Neuroterrain project, URL: http://www.neuroterrain.org)
and some with an aim toward being three-dimensional atlases (Toga et al., 1995).
The work of the Informatics Center of the Mouse Neu-
rogenetics (http://www.nervenet.org) includes a compre-
hensive library of Nissl-stained images of brains of over
100 strains of mice and a set of software tools for two-
and three-dimensional visualization and reconstruction
of different brain regions of interest.
Additionally, the
Edinburgh Mouse Atlas Project has made a significant
effort to create a gene expression database (Ringwald
et al., 1994) based upon the Atlas of Mouse Development
(Kaufman, 1992).
wide web sites: the High Resolution Mouse Brain Atlas
(http://www.hms.harvard.edu/research/brain), the Edin-
burgh Mouse Atlas Project (http://genex.hgu.mrc.ac.uk),
and the Mouse Brain Library (Rosen et al., 2003)
(http://www.mbl.org).
Software packages are available for visualizationof different data modalities and brain alignment
(the Neuroterrain project, URL: http://www.neuroterrain.org)
and some with an aim toward being three-dimensional atlases (Toga et al., 1995).
The work of the Informatics Center of the Mouse Neu-
rogenetics (http://www.nervenet.org) includes a compre-
hensive library of Nissl-stained images of brains of over
100 strains of mice and a set of software tools for two-
and three-dimensional visualization and reconstruction
of different brain regions of interest.
Additionally, the
Edinburgh Mouse Atlas Project has made a significant
effort to create a gene expression database (Ringwald
et al., 1994) based upon the Atlas of Mouse Development
(Kaufman, 1992).
free software Fusion Viewer
http://www.kgbtechnologies.com/fusionviewer/downloads.asp
Fusion Viewer is designed to allows researchers to easily examine multiple 3D data sets (ex. MRI, CT, SPECT, PET) simultaneously. Its main purpose is to provide a way to fuse multiple data sets so that they can be viewed as a single volume. Fusion Viewer displays the source data sets as three easily navigable orthogonal views through a volume, as a stack of 2D images, or as a 3D projection. Each volume is displayed in its own window so that you can arrange the volumes in the way that is most convenient for your work. Standard view controls such as intensity, resizing, and the application of LUT are provided. Multiple advanced dynamic range options for converting 16-bit data sets to 8-bits exist. Different fusion techniques and different projection techniques are implemented as plug-ins. Fusion Viewer is Freeware
Fusion Viewer is designed to allows researchers to easily examine multiple 3D data sets (ex. MRI, CT, SPECT, PET) simultaneously. Its main purpose is to provide a way to fuse multiple data sets so that they can be viewed as a single volume. Fusion Viewer displays the source data sets as three easily navigable orthogonal views through a volume, as a stack of 2D images, or as a 3D projection. Each volume is displayed in its own window so that you can arrange the volumes in the way that is most convenient for your work. Standard view controls such as intensity, resizing, and the application of LUT are provided. Multiple advanced dynamic range options for converting 16-bit data sets to 8-bits exist. Different fusion techniques and different projection techniques are implemented as plug-ins. Fusion Viewer is Freeware
free software MRIcro
http://www.sph.sc.edu/comd/rorden/mricro.html
MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms.
Features:
MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyse MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms.
Features:
- Converts medical images to SPM friendly Analyze format.
- View Analyze format images (big or little endian).
- Create Analyze format headers (big or little endian).
- Create 3D regions of interest (with computed volume & intensity).
- Overlap multiple regions of interest.
- Rotate images to match SPM template images.
- Export images to BMP, JPEG, PNG or TIF format.
- Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans).
Tuesday, May 20, 2008
Eleven Reasons Why Manuscripts are Rejected
Eleven Reasons Why Manuscripts are Rejected
Manuscripts submitted for peer review publication may be rejected for a number of different reasons, most of which are avoidable.
It should be noted that the reasons for accepting manuscripts are not the mirror image of the reasons for rejecting manuscripts. The main reasons for accepting manuscripts are: their contribution and relevance to the field, excellence of writing, and quality of the study design.
Many journals expect reviewers to assess the scientific merits and validity of research in submitted manuscripts; however, reviewers can become critical of manuscripts containing numerous language errors, which are difficult to eliminate without careful editing. Scientific writing demands both good science and well written manuscripts.
Following are the principal reasons why manuscripts are rejected. They are all equally important because reviewers tend to focus on different issues depending on their individual concerns and the journal's requirements.
1. Poor experimental design and/or inadequate investigation. An inadequate sample size, a biased sample, a non-unique concept, and scientific flaws in the study are common faults.
2. Failure to conform to the targeted journal. This is a common mistake. The focus of the manuscript is not within the scope of the journal and/or the guidelines of the targeted journal are not followed. This can easily be avoided by reading the targeted journal and reviewing the author guidelines.
3. Poor English grammar, style, and syntax. Though poor writing may not result in outright rejection of a manuscript, it may well influence the reviewer's and editor's overall impression of the manuscript. It has been shown that a well written manuscript has a better chance of being accepted.
4. Insufficient problem statement. It is important to clearly define and appropriately frame the study's question.
5. Methods not described in detail. Details are insufficient to repeat the results. The study design, apparatus used, and procedures followed must be made clear. In some cases it might be better to put too much information into the methods section rather than to put too little; information deemed unnecessary can always be removed prior to publication.
6. Overinterpretation of results. Some reviewers have indicated that a clear and ''honest'' approach to the interpretation of the results is likely to increase the chances of a manuscript being accepted. Identify possible biases and confounding variables, both during the design phase of the study and the interpretation of the results. Describe experimental results concisely.
7. Inappropriate or incomplete statistics. Using inappropriate statistical methods and overstating the implications of the results is a common error. Use an appropriate test and do not make the statistics too complicated. Quantify and present findings with appropriate indicators of measurement error or uncertainty (such as confidence intervals).
8. Unsatisfactory or confusing presentation of data in tables or figures. The tables or figures do not conform in style and quantity to the journal's guidelines and are cluttered with numbers. Make tables and graphs easy to read. Some editors may start by looking quickly at the tables, graphs, and figures to determine if the manuscript is worth considering.
It should be noted that the reasons for accepting manuscripts are not the mirror image of the reasons for rejecting manuscripts. The main reasons for accepting manuscripts are: their contribution and relevance to the field, excellence of writing, and quality of the study design.
Many journals expect reviewers to assess the scientific merits and validity of research in submitted manuscripts; however, reviewers can become critical of manuscripts containing numerous language errors, which are difficult to eliminate without careful editing. Scientific writing demands both good science and well written manuscripts.
Following are the principal reasons why manuscripts are rejected. They are all equally important because reviewers tend to focus on different issues depending on their individual concerns and the journal's requirements.
1. Poor experimental design and/or inadequate investigation. An inadequate sample size, a biased sample, a non-unique concept, and scientific flaws in the study are common faults.
2. Failure to conform to the targeted journal. This is a common mistake. The focus of the manuscript is not within the scope of the journal and/or the guidelines of the targeted journal are not followed. This can easily be avoided by reading the targeted journal and reviewing the author guidelines.
3. Poor English grammar, style, and syntax. Though poor writing may not result in outright rejection of a manuscript, it may well influence the reviewer's and editor's overall impression of the manuscript. It has been shown that a well written manuscript has a better chance of being accepted.
4. Insufficient problem statement. It is important to clearly define and appropriately frame the study's question.
5. Methods not described in detail. Details are insufficient to repeat the results. The study design, apparatus used, and procedures followed must be made clear. In some cases it might be better to put too much information into the methods section rather than to put too little; information deemed unnecessary can always be removed prior to publication.
6. Overinterpretation of results. Some reviewers have indicated that a clear and ''honest'' approach to the interpretation of the results is likely to increase the chances of a manuscript being accepted. Identify possible biases and confounding variables, both during the design phase of the study and the interpretation of the results. Describe experimental results concisely.
7. Inappropriate or incomplete statistics. Using inappropriate statistical methods and overstating the implications of the results is a common error. Use an appropriate test and do not make the statistics too complicated. Quantify and present findings with appropriate indicators of measurement error or uncertainty (such as confidence intervals).
8. Unsatisfactory or confusing presentation of data in tables or figures. The tables or figures do not conform in style and quantity to the journal's guidelines and are cluttered with numbers. Make tables and graphs easy to read. Some editors may start by looking quickly at the tables, graphs, and figures to determine if the manuscript is worth considering.
9. Conclusions not supported by data. Make sure your conclusions are not overstated, are supported, and answer the study's questions. Be sure to provide alternative explanations, and do not simply restate the results.
10. Incomplete, inaccurate, or outdated review of the literature. Be sure to conduct a complete literature search and only list references relevant to the study. The reviewers of your manuscript will be experts in the field and will be aware of all the pertinent research conducted.
11. Author unwilling to revise the manuscript to address reviewer's suggestions. This can easily be resolved. Taking the reviewers' suggestions into account when revising your manuscript will nearly always result in a better manuscript. If the editor indicates willingness to evaluate a revision, it means the manuscript may be publishable if the reviewers' concerns could be addressed satisfactorily.
history quantum chemistry
In 1964, Hückel method calculations (using a simple LCAO method for the determination of electron energies of molecular orbitals of π electrons in conjugated hydrocarbon systems) of molecules ranging in complexity from butadiene and benzene to ovalene, were generated on computers at Berkeley and Oxford.[8] These empirical methods were replaced in the 1960s by semi-empirical methods such as CNDO.[9]
In the early 1970s, efficient ab initio computer programs such as ATMOL, GAUSSIAN, IBMOL, and POLYAYTOM, began to be used to speed up ab initio calculations of molecular orbitals. Of these four programs, only GAUSSIAN, now massively expanded, is still in use, but many other programs are now in use. At the same time, the methods of molecular mechanics, such as MM2, were developed, primarily by Norman Allinger.[10]
One of the first mentions of the term “computational chemistry” can be found in the 1970 book Computers and Their Role in the Physical Sciences by Sidney Fernbach and Abraham Haskell Taub, where they state “It seems, therefore, that 'computational chemistry' can finally be more and more of a reality.”[11] During the 1970s, widely different methods began to be seen as part of a new emerging discipline of computational chemistry.[12] The Journal of Computational Chemistry was first published in 1980.
Several major areas may be distinguished within computational chemistry:
----------
The simplest type of ab initio electronic structure calculation is the Hartree-Fock (HF) scheme, an extension of molecular orbital theory, in which the correlated electron-electron repulsion is not specifically taken into account; only its average effect is included in the calculation. As the basis set size is increased, the energy and wave function tend towards a limit called the Hartree-Fock limit. Many types of calculations (known as post-Hartree-Fock methods) begin with a Hartree-Fock calculation and subsequently correct for electron-electron repulsion, referred to also as electronic correlation. As these methods are pushed to the limit, they approach the exact solution of the non-relativistic Schrödinger equation. In order to obtain exact agreement with experiment, it is necessary to include relativistic and spin orbit terms, both of which are only really important for heavy atoms. In all of these approaches, in addition to the choice of method, it is necessary to choose a basis set. This is a set of functions, usually centered on the different atoms in the molecule, which are used to expand the molecular orbitals with the LCAO ansatz. Ab initio methods need to define a level of theory (the method) and a basis set.
The Hartree-Fock wave function is a single configuration or determinant. In some cases, particularly for bond breaking processes, this is quite inadequate, and several configurations need to be used. Here, the coefficients of the configurations and the coefficients of the basis functions are optimized together.
The total molecular energy can be evaluated as a function of the molecular geometry; in other words, the potential energy surface. Such a surface can be used for reaction dynamics. The stationary points of the surface lead to predictions of different isomers and the transition structures for conversion between isomers, but these can be determined without a full knowledge of the complete surface.
A particularly important objective, called computational thermochemistry, is to calculate thermochemical quantities such as the enthalpy of formation to chemical accuracy. Chemical accuracy is the accuracy required to make realistic chemical predictions and is generally considered to be 1 kcal/mol or 4 kJ/mol. To reach that accuracy in an economic way it is necessary to use a series of post-Hartree-Fock methods and combine the results. These methods are called quantum chemistry composite methods.
In the early 1970s, efficient ab initio computer programs such as ATMOL, GAUSSIAN, IBMOL, and POLYAYTOM, began to be used to speed up ab initio calculations of molecular orbitals. Of these four programs, only GAUSSIAN, now massively expanded, is still in use, but many other programs are now in use. At the same time, the methods of molecular mechanics, such as MM2, were developed, primarily by Norman Allinger.[10]
One of the first mentions of the term “computational chemistry” can be found in the 1970 book Computers and Their Role in the Physical Sciences by Sidney Fernbach and Abraham Haskell Taub, where they state “It seems, therefore, that 'computational chemistry' can finally be more and more of a reality.”[11] During the 1970s, widely different methods began to be seen as part of a new emerging discipline of computational chemistry.[12] The Journal of Computational Chemistry was first published in 1980.
Several major areas may be distinguished within computational chemistry:
- The prediction of the molecular structure of molecules by the use of the simulation of forces, or more accurate quantum chemical methods, to find stationary points on the energy surface as the position of the nuclei is varied.
- Storing and searching for data on chemical entities (see chemical databases).
- Identifying correlations between chemical structures and properties (see QSPR and QSAR).
- Computational approaches to help in the efficient synthesis of compounds.
- Computational approaches to design molecules that interact in specific ways with other molecules (e.g. drug design).
----------
Ab initio methods
The simplest type of ab initio electronic structure calculation is the Hartree-Fock (HF) scheme, an extension of molecular orbital theory, in which the correlated electron-electron repulsion is not specifically taken into account; only its average effect is included in the calculation. As the basis set size is increased, the energy and wave function tend towards a limit called the Hartree-Fock limit. Many types of calculations (known as post-Hartree-Fock methods) begin with a Hartree-Fock calculation and subsequently correct for electron-electron repulsion, referred to also as electronic correlation. As these methods are pushed to the limit, they approach the exact solution of the non-relativistic Schrödinger equation. In order to obtain exact agreement with experiment, it is necessary to include relativistic and spin orbit terms, both of which are only really important for heavy atoms. In all of these approaches, in addition to the choice of method, it is necessary to choose a basis set. This is a set of functions, usually centered on the different atoms in the molecule, which are used to expand the molecular orbitals with the LCAO ansatz. Ab initio methods need to define a level of theory (the method) and a basis set.
The Hartree-Fock wave function is a single configuration or determinant. In some cases, particularly for bond breaking processes, this is quite inadequate, and several configurations need to be used. Here, the coefficients of the configurations and the coefficients of the basis functions are optimized together.
The total molecular energy can be evaluated as a function of the molecular geometry; in other words, the potential energy surface. Such a surface can be used for reaction dynamics. The stationary points of the surface lead to predictions of different isomers and the transition structures for conversion between isomers, but these can be determined without a full knowledge of the complete surface.
A particularly important objective, called computational thermochemistry, is to calculate thermochemical quantities such as the enthalpy of formation to chemical accuracy. Chemical accuracy is the accuracy required to make realistic chemical predictions and is generally considered to be 1 kcal/mol or 4 kJ/mol. To reach that accuracy in an economic way it is necessary to use a series of post-Hartree-Fock methods and combine the results. These methods are called quantum chemistry composite methods.
spectra biomedical optics
spectra biomedical optics
http://omlc.ogi.edu/spectra/
- Aorta tissue
- Carbonized tissue
- Fat
- Hemoglobin
- Indocyanine Green
- IntralipidTM (10% lipid)
- Methylene Blue
- Melanin, by Steven Jacques
- Melanin by Rodolfo Nicolaus, a website on melanin that is FULL of information!
- Water
- 125 PhotochemCAD Spectra!
Literate programming _Donald Knuth
Literate programming _Prahl
Literate Programming is a system of programming pioneered by Donald Knuth that allows one to break programs into small chunks. Each chunk should be short enough (say less than ten lines of code) can be completely and clearly documented. These chunks are assembled into a file and then run through a preprocessor to get either a documentation file (suitable for typesetting) or a just straight code.A bunch of literate programming solutions exist, since there seems to be more interest in writing new literate programming systems than in actually using them. Everyone seems to have an opinion. Knuth’s ideas are set forth in an interview, a book, and published programs like the Stanford Graphbase. In my opinion only two systems are worth considering: noweb and cweb.
noweb is an extensible system intended for a Unix environment written by Norman Ramsey. It is language independent and allows the creation of HTML documentation files automatically. Most people now use noweb. I really like the fact that chunks are numbered by page and then alphabetically by location on the page: “10c” refers to the third chunk on page 10.
I don’t use noweb because porting it to the Macintosh was hopeless. It is written in Icon and C. In fact, I was unable to get the existing noweb port for the Mac to work.
The philosophy behind CWEB is that programmers who want to provide the best possible documentation for their programs need two things simultaneously: a language like TeX for formatting, and a language like C for programming. Neither type of language can provide the best documentation by itself. But when both are appropriately combined, we obtain a system that is much more useful than either language separately. [Taken from the CWEB-3.0 User's Manual.] There are at least three variants of cweb available.
http://www.bme.ogi.edu/~prahl/
http://omlc.ogi.edu/software/lp/
noweb
noweb is an extensible system intended for a Unix environment written by Norman Ramsey. It is language independent and allows the creation of HTML documentation files automatically. Most people now use noweb. I really like the fact that chunks are numbered by page and then alphabetically by location on the page: “10c” refers to the third chunk on page 10.
I don’t use noweb because porting it to the Macintosh was hopeless. It is written in Icon and C. In fact, I was unable to get the existing noweb port for the Mac to work.
cweb
The philosophy behind CWEB is that programmers who want to provide the best possible documentation for their programs need two things simultaneously: a language like TeX for formatting, and a language like C for programming. Neither type of language can provide the best documentation by itself. But when both are appropriately combined, we obtain a system that is much more useful than either language separately. [Taken from the CWEB-3.0 User's Manual.] There are at least three variants of cweb available.
- cweb
- The original, canonical cweb by Donald E. Knuth and Silvio Levy. The cweb system consists a manual and the programs ctangle and cweave. No development is planned, but it is supported and bugs will still be fixed. It works and I use it.
- cwebx
- cweb was a translation of the original web system for Pascal. Something was lost in the translation. Marc van Leeuwen decided to rewrite it and add some rational features.
- ctwill
- ctwill was hacked by Donald Knuth and is an extension of cweave. It allows mini-indicies on every two page spread. This is great because every variable that is not defined on a two page spread is indexed and the relevant reference is available. It produces great documentation, at the cost of being a pain in the neck.
http://www.bme.ogi.edu/~prahl/
http://omlc.ogi.edu/software/lp/
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