Wednesday, 12 June 2019

Natalie Lamb and the RNA-seq Analysis for Beginners

This blog post has been produced after a training course at the University of Sheffield "RNA-seq Analysis for Beginners Training course". It will cover:
  • Performing quality assessment on our fastq files
  • Aligning fastq files to the reference genome
  • Visualising the reads in IGV
  • Counting against a set of reference transcripts
This essentially means what to do with raw RNA data (fastq) using the steps: Quality Control (fastqc) - Alignment (hisat2) - Counting (htseq) - Differential Expression (deseq2) - Pathways using Galaxy.








Upload Data

In Galaxy, an open, web-based platform for data intensive biomedical research, search upload in the "tools" section on the left hand side and select "Upload File". On the right hand side, each data set will be red. When uploaded, this will turn green.


Quality Control

Click "View" (the small eye icon next to the green data set) to see the fastq file. Fastq files are text files that describe the sequence. Each "read" is described by four lines: the sequence ID, the sequenced read, a blank (+) and the quality score (a long series of jibberish).










The quality (Q) scores are representations of how confident we are that a particular base has been called correctly (the base call probability). Each symbol has a meaning using the ASCII code. Letters that are further along the alphabet indicate higher confidence. The Q score is worked out using the formula Q=−10log10p using software. Some examples of Q scores:

  • Q = 30, p=0.001
  • Q = 20, p=0.01
  • Q = 10, p=0.1

Tools such as "FastQC Report" will read this score and translate it into a format that makes more sense, such as the below image. Green=passes, red=fails. Search "FastQC Report Quality Reports" in the "Tools" search bar. Under the heading "Short read data from your current history" select the desired file using the icon on the right under this heading. Click "Execute". This will produce images such as the below for the data set you selected.




























As in the above image, the quality score will often decrease over time as reagents age, meaning that often the last 10 base pairs are cut off.

Using MultiQC will allow you to compare multiple data sets at the same time, rather than FastQC Report which only allows you to see one data set at a time. In "Tools" search and select "MultiQC". Under "Which tool was used generate logs?" select "FastQC". Then select all the files with the name "Raw Data" then click "Execute".


























Alignment

Alignment is for determining where each of the reads come from. This is because both the genome you are trying to work with and the genome which is for reference use (so has already been decoded, so to speak) have both been broken down into fragments to make it quicker to find matches.



To do it, search "HISAT2" in "Tools". In the data set I was using, under the heading "Select a reference genome" I had to select "S. cerevisiae Apr. 2011 (SaccCer_Apr2011/sacCer3) (sacCer3)" but this depends on the species being used. Under the heading "FASTA/Q file either select a single or multiple files that you want to complete alignment on then click "Execute". It will produce bam files. These files give the location where each read is lined to.

Under the heading "QNAME", there are the names (SN) of the sequences (chromosomes) used in alignment (e.g. chrI is chromosome number 1) and their length (LN).


The below is what all the heading mean:

























Under the "FLAG" heading there will be a number. This can be searched for using this website to find out what that specific number means.

Flagstat (search for it in "Tools") will calculate the flag for each read in the bam file and tabulate the results. Don't forget to select multiple files if you are working with more than one data set. In the below example, the aligned percentage is 99.95%.



Idxstats (search for it in "Tools") will report the number of reads mapping to each reference sequence (i.e. chromosome).

























To visualise the alignments, open Integrative Genomics Viewer (IGV), a different software from Galazya which is a "high-performance visualization tool for interactive exploration of large, integrated genomic datasets" (IGV, 2019). It is ofetn used as a first pass at visualising NGS data (Next generation sequencing is a new method for sequencing genomes at high speed and at low cost).

In Galaxy, download the bam files you created in Galaxy by clicking on the data set and then the save icon on the right-hand panel. Download both the Download data set and Download index buttons.

In IGC, click the drop down in the top left and select the organism who you are working with. The bit at the bottom shows the genes present in the reference organism you have selected (i.e. the reference genome that has already been decoded). Click "File" then "Upload" and select all your bam files.

 In the box next to the organism, you can select a specific chromosome to look at it. In the above example, I am looking at Chromosome 1. You can also use the mouse to drag left and right.


Counting

After alignment, the next step is to count the number of tomes a specific gene has been sequenced. Longer genes will get more reads because there is more of them (the entire gene doesn't have to match, just bits of them).

In Galaxy, search and select "UCSC Main table browser" in "Tools". I used the following settings:

  • Set clade to Other
  • Set genome to S. cerevisiae
  • assembly Apr. 2011
  • group Genes and Gene Prediction
  • track SGD Genes
  • region genome
  • output format GTF - gene transfer format (limited) and send output to Galaxy

Click "Get Output" and then "Send Query to Galaxy"

Then search and select "htseq-count" in "Tools". Select all the bam files and make sure that "GFF File" is on the correct organism. Then click "Execute".


Differential Expression 

The term differential expression was first used to refer to the process of finding statistically significant genes from a microarray gene expression study. RNAseq has now replaced microrrays, although they can still be used. Basically it means that you've counted the genes but now you need stats to prove you've the genes you've counted are all differentially expressed.

For example in the below image, A has a different average differential experession than B but there is variability/range.





























In Galaxy, search and select "DESeq2" in "Tools. I used the following parameters:

  • 1. Factor level: Input Batch
    • Count files: batch1-htseq, batch2-htseq
  • 2. Factor level: Input Chem
    • Select columns containing control: chem1-htseq, chem2-htseq
  • For Output normalized counts table select "Yes"
Click "Execute"





































Search and select "Filter" in tools. I used the following conditions:

  • Filter: DESeq2 results file
  • With following condition: c7 < 0.05 and (c3 > 1.0 or c3 < -1.0)
  • Number of header lines to skip: 1

Click "Execute". This will extract the significant differentially expressed genes, such as those below.




















Search "Column Join" using "Tools" and select all the htseq files. Click on this on the right hand side and click save to download this file.

Degust is a web tool that can analyse the counts files produced in the step above, to test for differential gene expression. It offers and interactive view of the differential expression results. Upload the file created by clicking "Upload your counts file". I used the following parameters:
  • For "Name" type “DGE in SaCer3” (or whatever you want to call the analysis)
  • For "Info Columns" select “#KEY”
  • For "Analyze Server Side" leave box checked.
  • Click "Add Condition" and name the different conditions e.g. "Batch" and "Chem"
  • Save the settings and then click "View The Results"





















The website Venny computes overlaps in gene lists so this could wither be between experiment conditions (e..g. batch vs chem) or through genes identified using different methods (e.g. DESeq2 and Degust). Open both the DESeq2 and Degust results files in Excel. Copy the names (e.g. YAR002C-A) of the DESeq2 data set which have a p-value less than 0.05 into the top-left box on the Venny website (List 1). Do the same for the names of the Degust data set, again with a p-value less than 0.05 into List 2. 

And there we have it, how to do some basic RNA-seq analysis!


References
  1. Dunning, M (2019), Hands-on RNA-seq Analysis in Galaxy, based on the RNA-Seq Workshop by Melbourne Bioinformatics written by Mahtab Mirmomeni, Andrew Lonie, Jessica Chung Original, modified by David Powell (Monash Bioinformatics Platform), further modified by Mark Dunning of Sheffield Bioinformatics Core.
  2. Nookaew I, Papini M, Pornputtpong N, Scalcinati G, Fagerberg L, UhlĂ©n M, Nielsen J (2010), A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae. Nucleic Acids Res 2012, 40 (20):10084 – 10097. doi:10.1093/nar/gks804. 
  3. Guirguis A, Slape C, Failla L, Saw J, Tremblay C, Powell D, Rossello F, Wei A, Strasser A, Curtis D (2016), PUMA promotes apoptosis of hematopoietic progenitors driving leukemic progression in a mouse model of myelodysplasia. Cell Death Differ. 23(6).

Friday, 24 May 2019

Natalie Lamb and the referencing guide for school pupils

Today I delivered my eight Tutorial 6 with The Brilliant Club, this time at Deepings School. In this session I deliver 1:1 feedback about the draft final assignments that have been submitted to me. A reoccurring point of discussion was the formatting of referencing. I produced this guide and activity on how to reference for KS3 pupils but it could equally be used with older or younger pupils. A free PDF document of this guide and an in-class or homework activity that can be printed and used in class can be found using this link.


Natalie’s Guide on How to Reference
You should reference anything that has not come from your own mind. 
It is OK to do it slightly differently than the below, just make sure all your references have the same format. Don’t forget to reference images/graphs too! If you look under the heading “Books:” you will see the proper way to reference the Brilliant Cub handbook.

Referencing in your essay
In your final assignment, do a short reference. This means you are proving the information is true and from a reliable source but not interrupting the flow of your essay by adding loads of text. Instead, people reading your work can look up the full reference using the bibliography at the end of your work.

Examples: 

  • BBC (2017) said “water is the most useful thing in the world”.
  • This was also discussed by BBC (2017), who said “water is the most useful thing in the world”.
  • BBC (2017) said “water is the most useful thing in the world”, which means the BBC thinks water is great.
  • In the world, water is useful because it helps people (BBC, 2017).
  • Some experts say that water is very helpful (BBC, 2017).



Referencing at the end of your essay
At the very end of your essay, you should use the heading Bibliography. The bibliography is where all the references are written in full in a list in alphabetical order. There are slightly different ways of writing the reference, depending on what the source is (for example, a website, a book, a journal paper).

Website:

  • Structure
    • Last name, First initial (Year published), Website Title, URL (Accessed: Day/Month/Year)
    • Company (Year published), Website Title, URL (Accessed: Day/Month/Year)
  • Example 
    • City of Toronto (2017), How does lake water get turned into drinking water?,https://www1.toronto.ca/wps/portal/contentonly?vgnextoid=baa807ceb6f8e310VgnVCM10000071d60f89RCRD (Accessed: 23/08/17) 


Book:

  • Structure
    • Last name, First initial (Year published), Title. Edition. (Only include the edition if it is not the first edition) City published: Publisher, Page(s)
    • Company (Year published). Title. Edition. (Only include the edition if it is not the first edition) City published: Publisher, Page(s)
  • Example
    • Lamb, N (2017), From distant rivers to your kitchen sink: The chemical, microbiological and civil engineering journey of drinking water treatment, Brilliant Club Handbook, pp 17


Journal Paper:

  • Structure
    • Last name, First initial (Year published), Article title, Journal, Volume (Issue), Page(s)
  • Example
    • Ross, N (2015), On Truth Content and False Consciousness in Adorno’s Aesthetic Theory, Philosophy Today, 59(2), pp. 269-290


Example bibliography:

Bibliography

City of Toronto (2017), How does lake water get turned into drinking water?,https://www1.toronto.ca/wps/portal/contentonly?vgnextoid=baa807ceb6f8e310VgnVCM10000071d60f89RCRD (Accessed: 23/08/17)
Lamb, N (2017), From distant rivers to your kitchen sink: The chemical, microbiological and civil engineering journey of drinking water treatment, Brilliant Club Handbook, pp 17
Ross, N (2015), On Truth Content and False Consciousness in Adorno’s Aesthetic Theory, Philosophy Today, 59(2), pp. 269-290



References Test



Thursday, 23 May 2019

Natalie Lamb and the APM Project Management Qualification: Project lifecycle from procurement to termination

Members of my team recently attended a course on project management so I borrowed the APM Project Management Qualification Study Guide (2014) to give myself a bit of an insight into project management and how it links into PhDs or other similar research. This post is part of a series of posts I have produced to better split project management into a few easily digestible sections. This post is on Product lifecycle from procurement to termination but there are other posts on What is a project, Project roles and responsibilites, Why do project management?, Conflict and communication, Leadership and motivation and Health and Safety and risk assessment. Please use the links to get to your post of interest.


Procurement
  • Procurement = how an organisation acquires its goods and services
  • Procurement strategy = how the project will procure and manage goods and services 
  • Includes: make or buy decision (e.g. could the goods be made in house cheaper?), contractual relationship (buy from one supplier or many?), reimbursement methods, supplier selection 
  • Types of contractual relationships
    • Single contracts- single client, single supplier, single contractor 
    • Parallel contracts- multiple single contracts with a number of contractors 
    • Sequential contracts- one supplier doing one task then another doing one after
    • Prime and subcontracts- one main supplier who sources others
    • Turnkey contracts- single supplier provides all goods and services
    • Partnering- two/+ organisations work together to achieve the project 
  • How to select suppliers
    • Research the market
    • Pre-qualify suppliers- reduce the list of potential supplier to a manageable number
    • Issue an invitation to tender
    • Answer questions the bidders have raised
    • Receive and evaluate bids and review against selection criteria
    • Award a contract

Types of project review
  • Gate reviews
    • A formal review usually commissioned by the sponsoring organisation
    • A formal checklist with the outcomes of pass/pass with reservation/fail
    • Helps track progress and form relationships
  • Post project review
    • Carried out as soon as the project is finished to capture lessons learned
    • Will consider the normal success criteria, effectiveness of the project management methods, tools, practises and team performance
  • Benefits realisation reviews
    • After the products and handover completed so a full evaluation of the benefits can be done
    • Managed and chaired by the sponsor
    • To assess the achievement of the stated benefits in the business case
  • Stage reviews
    • During the project to assess progress using key performance indicators (KPIs)
    • Convened by the project manager, supported by the team, chaired by the sponsor and uses 
  • Peer reviews

Quality control 
  • Quality = an assessment of a product’s fitness for purpose
  • Quality plan includes: roles and responsibilities concerned with quality, the processes used, continual improvement, project assurance techniques, quality control techniques, interactions with other processes
  • Quality assurance = demonstrated and providing confidence to all stakeholders that quality requirements will be achieved
    • Incorporates: training, audits, lessons learnt, supplier accreditation 
  • Quality control 
    • Can include: inspection and measurement, walk-throughs (more in-depth than inspection and measurement), pareto analysis (understanding the nature and root causes of observable faults), process control charts (e.g. how sample product has varied over time)
  • Quality management benefits: prevents problems, gives stakeholders confidence they are getting what they have asked, reduces rework to save on costs, reduces risks, improves efficiency

Project lifecycle
  • Project lifecycle = the evolutionary progression through the phases of a project and the broad flow of the project 
  • Helps to demonstrate progress and review future work to be completed
  • The concept phase- everything up to and including the production of the business case, overseen by the sponsor
  • The definition phase- production of a project management plan
  • The development phase- the construction of the components needed for the end product, as set out in the project management plan, which may include different stages and stage reviews for progress evaluation
  • Handover- commissioning the products by project team
    • Formal hand over the deliverables to the users and make sure they have everything in place to cope with any issues in the short term (long term, the users have to cope without assistance)
    • Create operating procedures
    • Have a form of final acceptance
  • Closure- the closure of the project and disbanding of the project team 
    • Ensure users know how to operate products 
    • Can also include an extended project life cycle, including a benefits realisation phase and an investigation into operations
  • Termination- how much it will cost to dispose of the product at the end of its useful life 

Glossary
  • APM = Association for Project Management
  • Procurement = how an organisation acquires its goods and services
  • Procurement strategy = how the project will procure and manage goods and services 
  • Quality = an assessment of a product’s fitness for purpose
  • Project lifecycle = the evolutionary progression through the phases of a project and the broad flow of the project 
  • KPI = key performance indicator

References
  • Association for Project Management (2014), APM Project Management Qualification Study Guide, Association for Project Management, Buckinghamshire.

Natalie Lamb and the APM Project Management Qualification: Health and Safety and risk management

Members of my team recently attended a course on project management so I borrowed the APM Project Management Qualification Study Guide (2014) to give myself a bit of an insight into project management and how it links into PhDs or other similar research. This post is part of a series of posts I have produced to better split project management into a few easily digestible sections. This post is on Health and Safety and risk assessment but there are other posts on What is a project, Project roles and responsibilites, Conflict and communication, Why do project management?, Leadership and motivation and Product lifecycle from procurement to termination. Please use the links to get to your post of interest.



Project Health and Safety 

  • Make sure the health, safety and environment plan is in place
    • Includes: project scope, roles and responsibilities, external standards, reporting mechanisms, project-related procedures, keeping records of training etc.
    • Developed in conjunction with stakeholders in the sponsoring organisation
    • Approved by the relevant health safety and environmental body in the sponsoring organisation 
  • Make sure risk assessments are carried out, funded, properly recorded and actions completed 
    • Don’t have to carry it out themselves but need to make sure it is done
  • Have a properly trained team
  • Ensure there is open and honest disclosure so staff are comfortable reporting problems
  • Report near misses (RIDDOR/ Reporting of injuries, disease and dangerous occurrences regulations)
  • Complete regular reviews so minor situations don’t become more serious 
  • Make everyone aware of the threat of stress, which is a HSE concern 
    • Ensure working hours are reasonable
    • Proper relaxation facilities should be available
    • Project team should be consulted when work is being allocated 
  • Ensure proper safety equipment is provided, potentially using a code of practise to check the minimum requirements
  • Address environmental issues including: prevention, re-use, recycle, recovery, disposal


Potential risks
  • Risk = “A risk event is an uncertain event or set of circumstances that, should it occur, will have an effect on the achievement of one or more of the project’s objectives.” (AMP, 2004)
  • Environmental factors can influence a project and the more aware a project manager is of them, the easier they can be prepared for and managed
  • Can include: political (e.g. political influences, politically motivated stakeholders), economic, sociological, technological, legal (e.g. health and safety, GDPR), environmental (PESTLE)
  • Other considerations: procurement processes, regulatory requirements, use of structured methods, the organisations’ appetite for risk, the organisation’s strengths, weaknesses, opportunities and threats 

The purpose of risk management plans
    • Define how risks are dealt with
    • Get improvement through feedback
    • Have contingencies in place
    • Ensure the project management plan is being followed
    • Everyone understands what the potential risks are

The APM risk management process:
  • Initiation of plan
    • Includes: scope of risk management, objectives of plan (e.g. which risk reduction is planned), roles, process (for risk identification, assessment and management), tools
  • Identification of risks
    • E.g. by using brainstorming, interviewing, Delphi (debate), prompt lists, checklists, assumptions analysis
    • Recorded on a risk log, including: ID number, description, category (strategic/project/operational/technical), potential impact, potential impact after mitigation, potential actions to mitigate risk, assignment of owner
  • Assess risks 
    • Asses risks quantitatively using a risk score 
  • Plan responses
    • Especially for the higher risk risk events
    • To reduce the probability of the risk occurring and put in place contingencies if it does still occur
    • E.g. with threats: accept the risk with no proactive action, avoid the risk by changing the approach, transfer the risk onto someone else’s risk log, reduce the probability or the impact
    • E.g. with opportunities: reject an opportunity because it requires too much time or work, enhance the probability of an opportunity occurring, exploit by changing the scope of a project to get an extra benefit for the stakeholders, share an opportunity with others
  • Implement responses 


Glossary
  • APM = Association for Project Management
  • RIDDOR = Reporting of injuries, disease and dangerous occurrences regulations 
  • HSE = Health and Safety Executive (a government agency)
  • Risk = “A risk event is an uncertain event or set of circumstances that, should it occur, will have an effect on the achievement of one or more of the project’s objectives.”
  • GDPR = The EU General Data Protection Regulation
  • PESTLE = political, economic, sociological, technological, legal, environmental 

References
  • Association for Project Management (2014), APM Project Management Qualification Study Guide, Association for Project Management, Buckinghamshire.
  • Association for Project Management (2004), Project Risk Analysis Management (PRAM) Guide, 2nd edition, Association for Project Management, Buckinghamshire.


Natalie Lamb and the APM Project Management Qualification: Leadership and motivation

Members of my team recently attended a course on project management so I borrowed the APM Project Management Qualification Study Guide (2014) to give myself a bit of an insight into project management and how it links into PhDs or other similar research. This post is part of a series of posts I have produced to better split project management into a few easily digestible sections. This post is on Leadership and motivation but there are other posts on What is a project, Project roles and responsibilites, Conflict and communication, Why do project management?, Health and Safety and risk assessment and Product lifecycle from procurement to termination. Please use the links to get to your post of interest.


Why is good leadership important?
  • Prevents interpersonal conflict
  • Prevents high staff attrition rates
  • Makes it easier to recruit staff
  • Improves absence and sickness rates
  • Likely to produce a better quality of work

What makes a good leader?

  • “Leadership is the ability to establish vision and direction, to influence and align others towards a common purpose, and to empower and inspire people to achieve success.” APM (2012).
  • Help maintain and promote project’s vision
  • Have energy, drive and commitment to motivate the team
  • Reinforce positive relationships
  • Build a productive project and working environment
  • Raise morale with clear achievable goals
  • Act as a coach/mentor to encourage personal growth
  • Help resolve exceptional events
  • Provide productive and constructive feedback
  • Protect the project from unwarranted external criticism
  • Lead with a different focus at different times

Things staff need before they can be motivated
  • Supervision
  • Adequate work conditions
  • Acceptable company policies
  • Salary
  • Civility and professionalism in peer relationships

How to motivate staff
  • Achievement- being able to achieve at your job, having short clear definite targets
  • Recognition- having people seek your opinion
  • Work- enjoying your job
  • Responsibility- having responsibility for your work
  • Advancement- new challenges
  • Growth- e.g. new skills, contacts, career ambitions

How to motivate stakeholders

  • Stakeholder = has a vested interest in the outcome of a project
  • Process: identify, assess, develop, engage, manage
  • Identify- who are the stakeholders?
  • Assess- who are the influential people?
    • Use a stakeholder management plan to determine who are/who you want to be high power high interest stakeholders
  • Develop communication plans
  • Engage and influence stakeholders
    • Enact the plan and make sure it worked
  • Manage stakeholder expectations
    • Better understand the risks, benefits and user requirements
  • Identify groups against the project
    • To acknowledge the influence of the organisation on success

Stakeholder Engagement Plan

Glossary
  • APM = Association for Project Management
  • Leadership  = the ability to establish vision and direction, to influence and align others towards a common purpose, and to empower and inspire people to achieve success. (APM, 2012)
  • Stakeholder- has a vested interest in the outcome of a project

References
  • Association for Project Management (2014), APM Project Management Qualification Study Guide, Association for Project Management, Buckinghamshire.
  • Association for Project Management (2012), Body of Knowledge, 6th edition, pp68, Association for Project Management, Buckinghamshire.

Natalie Lamb and the APM Project Management Qualification: Conflict and communication

Members of my team recently attended a course on project management so I borrowed the APM Project Management Qualification Study Guide (2014) to give myself a bit of an insight into project management and how it links into PhDs or other similar research. This post is part of a series of posts I have produced to better split project management into a few easily digestible sections. This post is on Conflict and communication but there are other posts on What is a project, Project roles and responsibilites, Why do project management?, Leadership and motivation, Health and Safety and risk assessment and Product lifecycle from procurement to termination. Please use the links to get to your post of interest.


What happens when project communications go wrong?
  • Different people get different messages, resulting in doubt, concern, confusion and rework
  • Costs are not automatically included in the budget
  • Stakeholder needs, risks, benefits and costs not fully appreciated

Potential barriers to project communication
  • Too much jargon/technical language altering the receiver's perception of what is being said
  • Environment not fit for purpose
  • Lack of empathy for receiver’s attitude/personal state
  • Selective listening
  • Time zones/geography
  • Culture/language
  • Distractions/other priorities 

What to do when communications go wrong: dealing with conflict
  • Avoiding- don’t want to get involved with the situation
  • Accommodating- go along with what is being proposed without challenge, which can lead to wrong ideas being developed
  • Competing- try to get their own way
  • Collaborating- ideal situation
  • Compromising- will sacrifice some of what they want to get a deal 

 Thomas-Kilmann model (1992)

      
Negotiation
  • Negotiation is a process for reaching agreement, where conflict may occur
  • It can be formal, informal, competitive (e.g. haggling), collaborative (the ideal, as both parties get more than could be achieved alone)
  • Process- understand the need for negotiation---planning (understand the other side’s position and know who has the power to make the decision)---discussion---proposal and agreement---review (is the agreement being acted on?, lessons learnt)

Glossary
  • APM = Association for Project Management
  • Negotiation = a process for reaching agreement, where conflict may occur 

References
  • Association for Project Management (2014), APM Project Management Qualification Study Guide, Association for Project Management, Buckinghamshire.
  • Thomas and Kilmann (1992), Thomas-Kilmann Conflict Mode Instrument, Tuxedo, New York.

Natalie Lamb and the APM Project Management Qualification: Why do project management?

Members of my team recently attended a course on project management so I borrowed the APM Project Management Qualification Study Guide (2014) to give myself a bit of an insight into project management and how it links into PhDs or other similar research. This post is part of a series of posts I have produced to better split project management into a few easily digestible sections. This post is on Why do project management? but there are other posts on What is a project, Project roles and responsibilites, Conflict and communication, Leadership and motivation, Health and Safety and risk assessment and Product lifecycle from procurement to termination. Please use the links to get to your post of interest.


Project management methodology
  • The procedural framework within which the project can operate
  • Can consist of public project management methodologies or methods within an organisation
  • Includes: individual roles, the product, process/framework that need to be followed, documentation templates (e.g. for the project management plan, risk log and product specifications), tools that can be deployed (e.g. software)
  • Advantages
    • Provides a link to organisational governance
    • Requires thought about how to project fits with the organisation
    • All projects completed in the same way improving: consistency, continuity, communication, clarity and capability

The advantages of project management
  • It makes projects consistent, with consistent processes and approaches
  • Risk is reduced and opportunities are maximised because of consistent processes and experienced project managers
  • Risks can be managed proactively and with enough time to consider these risks

The disadvantages of project management
  • May need to recognise that the programme manager is the sponsor, particularly if they are part of a larger programme structure
  • The programme will usually install its own governance arrangements on projects, which the project manager would have to conform to
  • Project manager may not be trained on the specific method used to govern the programme
  • Reliant on managerial meetings to co-ordinate tasks with other project managers
  • Project manager may feel distant from the customer because the products are delivered to the client through the programme, which can cause misinterpretation and confusion 

Glossary
  • APM = Association for Project Management
  • Project Manager = managers the project so it follows the project management plan
  • Project = an enterprise that is carefully planned to achieve a particular aim
  • Project Management Plan = The procedural framework within which the project can operate

References
  • Association for Project Management (2014), APM Project Management Qualification Study Guide, Association for Project Management, Buckinghamshire.