BSc Project

If you need access to the United States pharmacopoeia (USP) then you can get it by logging in through the IT Tallaght Library website. You can find the USP on the page at the link below. Just search for pharmacopoeia at the link below and click it. You will then be required to login using your IT Tallaght student details.

http://bit.ly/usptallaght

 

RefME is a platform I have talked about before as a useful piece of kit for managing your referencing. RefME has been purchased by another reference manager which has both free and premium (pay to use) versions called Cite this for me. RefME will shut down in due course so it might be worth considering moving to another manager. Cite this for me is a very simple to use reference manager but there are quite a few programs out there which offer both free and premium versions. A list of my top reference managers can be found below:

Zotero has chrome plugins to assist reference capture.

January 2017 Exam Timetables are now available here:

http://www.it-tallaght.ie/examtimetables

The Openstax organisation offer free books that are peer-reviewed by scientists and other academic individuals. There are currently a number of books available by them related to biology but they have now launched a new microbiology book well worth having a read of. It may help you with your studies. You can download the Microbiology book at the link below:

https://d3bxy9euw4e147.cloudfront.net/oscms-prodcms/media/documents/Microbiology-OP.pdf

This image below outlines the step by step process for HPLC Method Development.

Method Development

Courtesy: Researchgate

Agilent has a few nice guides on HPLC which I’ve attached below.

Agilent HPLC Basics

Agilent HPLC Separation Fundamentals

Agilent Rapid HPLC Method Development

Ray D’arcy had Prof. Michael Barry of the NCPE (National Centre for Pharmacoeconomics) on his radio show. Prof. Barry discussed the recent orkambi decision and the role the NCPE has in the national formulary. Really interesting conversation and well worth a listen. The podcast can be downloaded from the link below:

NCPE on Ray D’arcy

One of your colleagues found a very good book on Pharma Science on the web and it’s available free. The title of the book is: Pharmaceutics: The Science of Dosage Form Design 2nd Edition By Micheal E. Aulton and can be found at the link below.

http://bit.ly/pharmascienceebook

Below are two links to sets of videos giving very basic explanations of how various chromatographic methods work.

Chromatographic Methods:

Mr Simple Science:

The link below will take you to a very useful bit of software created using excel that allows you to explore the effects of various parameters on the elution profile of a product. You can play around with column length, elution method (gradient or isocratic), injection volume, temperature and much more and see their effect on resolution and retention time. The first link gives a good overview of the software’s capabilities and the second link is to the program itself which you can download for free and run on PC or Mac.

Among the offered possibilities, it allows you to:

  1. Illustrate the concept of chromatographic resolution including the impact of retention, selectivity and efficiency on resolution.
  2. Understand the van Deemter equation and kinetic performance in HPLC.
  3. Recognize the importance of analytes lipophilicity (log P) on retention and selectivity in reversed phase HPLC mode (RPLC).
  4. Handle the RPLC retention, taking into account the acido-basic properties (pKa) of compounds and mobile phase pH.
  5. Simulate the impact of mobile phase temperature on HPLC separations
  6. Understand the behavior of a mixture of diverse compounds in both isocratic and elution gradient modes.
  7. Show the influence of instrumentation (injected volume and tubing geometry) on kinetic performance and sensitivity in HPLC.
  8. Demonstrate the impact of analytes molecular weight on thermodynamic (retention and selectivity) and kinetic (efficiency) performance.

The website below is a great resource for staying current on topics in relation to liquid chromatography and gas chromatography. Sections of the site include:

  • Publications on LC and GC systems
  • Information on techniques including:
  • LC
  • HPLC
  • UPLC
  • GC
  • Mass Spec
  • Sample Prep
  • LC/GC Television and Multimedia
  • eBooks (Free)

http://bit.ly/lcgcresource

Below is a link to some interesting review papers on HPLC/LC systems. Well worth a read to help you better understand the topic. Explore more on your own by visiting pubmed.gov. Remember to use the filters on the left hand side of the page to help you narrow your searches.

http://bit.ly/hplcpapers

As an update to a previous post on this please note there is a newer and more often updated free desktop publishing software known as Libreoffice. Not everyone has or can afford Microsoft Office but there are plenty of free packages out there that do much the same as Microsoft office and are similarly easy to use. You can get a free office suite of programs from many companies and organisations but one of my favourites is Libre Office. Select the version open office for your system here:

https://www.libreoffice.org/download/libreoffice-fresh/

Below are two videos showing what goes into the process of fermentation, where the cells produce the product (part 1), to product separation and recovery (part 2). These illustrate many of the aspects we are discussing in class.

Clinical trial details that the US FDA is monitoring can be found at http://clinicaltrials.gov but if you want to see what’s happening in Europe check out http://clinicaltrialsregister.eu The European only launched recently (January 2016).

EU Clinical Trials Register

 

The animations below will show you how both PCR and RT-PCR work.

The PCR instructional animation can be found at this link. You can either watch and interact with it on the page or download it for Mac or PC at the links on the page.

https://www.dnalc.org/resources/animations/pcr.html

 

The interactive RT-PCR instructional animation can be found at the link below.

http://www.bio.davidson.edu/courses/Immunology/Flash/RT_PCR.html

Scitable is a website run by Nature Publishing Group which provides biology students with resources on genetics and cell biology. It has great images, explanations (definitions), articles and much much more on everything to do with biology. Well worth checking out if you’re studying for exams or researching for assignments.

http://www.nature.com/scitable

2016-02-23_07-26-24

 

The links below are to some tips on how to plan and deliver a presentation on you project. I’ve also attached a “rough” template of a PowerPoint presentation you could use to help you with your planning. Feel free to come up with some nice designs of your own.

Presentation Tips

PowerPoint Presentation Sample Template

There’s a Moodle mobile app available for iOS and Android devices. It might be useful accessing information away from your PC/Mac. The apps are available from the links below:

iOS

Android

 

RefME is a free reference manager. It can help you capture references on the web and put them together into file format you can export and use in your thesis submission or project submission. For some general info on how it works and what it’s compatible with see this earlier post on LectureHub here. The video below will show you how to capture references on ncbi.nlm.nih.gov/pubmedbiopharminternational.com and books.google.ie to start with but it can do so much more. Well worth considering using it to help you with your thesis/essay writing.

RefME is a free reference manager that works as an add-on to a desktop browser and also as a mobile app. It is available as an app for iOS and Android. With the apps you can scan barcodes of books or search for references and then add them to your account.

It also works with Google Chrome Browser. This app and browser plugin will help you capture (from pubmed or any other web page where you have a potential reference) and manage references to go into your thesis. Once you’ve captured your references and used them in your thesis you can then export all references in the proper format (Harvard is probably the best format) and copy and paste them into your thesis.

You can sign up with a google or facebook account plus it’s completely free. More info can be found at the link below and I’ll put together a short video on how to use it later this week.

http://the12appsofchristmas.zohosites.com/App7.html

If you’re looking for past papers for any subject you are studying you can get them from the ITT Dublin Library website at this link:

http://millennium.it-tallaght.ie/search/r

 

 

The ITT Dublin Library has an agreement with openstax college who have made available a number of free books covering many subjects.

The full list of books can be found here:

https://www.openstaxcollege.org/books

I have reviewed the Biology, Microbiology and Concepts in Biology books and think they are all well written and applicable to the course. If you need to read extra material to help you understand your notes I can wholeheartedly recommend them. If you’ve any queries just give me a shout.

Biology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/biology

Concepts in Biology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/concepts-of-biology

Microbiology:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/microbiology

Chemistry:

http://0-openstaxcollege.org.millennium.it-tallaght.ie/textbooks/chemistry

Polymixins are a type of antibiotic of which Colistin is one. Polymixins and in particular colistin are one of our last lines of defense against serious bacterial infection. While resistance has been seen against these antibiotics it has only occurred through mutations in the chromosome of the bacteria making resistance difficult to pass on to other bacteria. A new research article in The Lancet Infectious Diseases has reported that, for the first time, resistance to colistin has been detected on a plasmid. This is of significance as bacteria can transfer/share plasmids readily and thus spread resistance much more quickly then through mutations in the chromosome.

This raises the real possibility of the emergence of untreatable diseases. Are we at the beginning of a new era of bacterial superiority?

http://www.bbc.com/news/health-34857015

The links below describe in detail how to use either Harvard or Vancouver referencing styles for writing an essay/thesis. Harvard is probably the easier to use especially if you don’t have a reference manager program. This is due to the fact that it is very forgiving if you need to add additional detail to the article. Instead of having to re-number ever reference if you used Vancouver style, you can just add the surname and year to the new reference and just put the references in alphabetical order at the end of the article.

The most important thing to remember with referencing is to be consistent with what ever style you use. Use of web links is never appropriate for referencing!

IT- Tallaght

Harvard Style

Guide to Writing Styles and Citing Sources

 

UCD

Harvard Style Guide

Vancouver Style Guide

Not everyone has or can afford Microsoft Office but there are plenty of free packages out there that do much the same as microsoft office and are similarly easy to use. You can get a free office suite of programs from many companies and organisations but one of my favourites is Open Office. Select the version open office for your system here:

https://www.openoffice.org/download/index.html

Peer reviewed material is material published in scientific journals (or other types of journals). These articles have been published in these journals only following review of the articles by other scientists who assess the quality and validity of the material.

News articles and websites are not peer reviewed and anyone can right anything there whether it is true or not. In scientific essays you should focus on referencing peer reviewed material first and foremost before utilising other material.

Sample paragraph showing multiple references:

“TLR3 recognizes viral dsRNA and endogenous dsRNA derived from necrotic cells during inflammation (11, 12). In humans, defective TLR3 function has been associated with enhanced susceptibility to viral infection and in particular, herpes simplex encephalitis (13). Recently, a functional TLR3 polymorphism, Leu412Phe (TLR3 L412F, rs3775291) was described which results in attenuated NF-B- and IRF3-signaling in affected cells (14). TLR3 412F has also been shown to confer protection against geographic atrophy in macular degeneration by attenuating TLR3-induced retinal epithelial cell apoptosis (15).”

References should be used throughout the essays. The above piece is in Vancouver Style. Other referencing styles can be found here. Details of what Vancouver style is and how to use it for different types of references can be found here:

Vancouver Style

Plagiarism includes:
  1. Using another author’s words without proper citation
  2. Using another author’s ideas without proper citation
  3. Citing a source but reproducing the exact word without quotation marks
  4. Borrowing the structure of another author’s phrases/sentences without giving the source
  5. Borrowing all or part of another student’s paper
  6. Using paper-writing service or having a friend write the paper

Avoid using significant amounts of quotes to in your essay as this is not appropriate. Put things you’ve read and understand in to your own words.

The website Pharmacology Corner looks to me to be a great resource for drug discovery, targets and receptors information. Well worth checking out to help with your studies and essays.

2014-09-30_11-49-41

The links below are to resources you can use which will help you with your literature surveys/essays or studies in general.

ITT Dublin Library Medscape
The Cochrane Library Google Scholar
National Library of Medicine Web of Science
Google Books FDA
Clinical Trials HPRA
Biocheminternational  PharmaTech

 

This is advice taken from Carlton University in Canada from their department of economics but it is very useful in general for writing academic essays.

Academic Essay Writing

Research papers are a great resource for learning. One of the largest databases of peer reviewed published research papers is housed by the US National Library of Medicine National Institutes of Health. You can find specific papers on techniques or new discoveries or review papers which offer a broad look at a particular topic. This should be your first stop for research on topics we’re discussing in lectures or for your assignments.

http://www.ncbi.nlm.nih.gov/pubmed/

This book by the US department of health and human sciences “Inside the Cell” is freely available on Google Books and offers a really nice explanation of the entire eukaryotic cell and all it’s components. Well worth a read.

You can have a look at it on Google Books here or download the pdf version from here

As well as the books in the library Google Books can offer a great resource for learning about biology.